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/7901150/working' mkdir: created directory `/scratch/stefan/7901150/working/protonate' Storing results in /scratch/stefan/7901150/finished Working in /scratch/stefan/7901150/working /scratch/stefan/7901150/working /scratch/stefan/7901150 /scratch/stefan/7901150/working/protonate /scratch/stefan/7901150/working /scratch/stefan/7901150 Precomputing protomers for all compounds (pH: 7.4) ph 7.4: 533 protomers created Coalesing and merging protomers 483 protomers generated for 448 compounds Checking for new stereocenters and expanding 484 protomers after new stereo-center expansion /scratch/stefan/7901150/working /scratch/stefan/7901150 Bulk generating 3D conformations all protomers in /scratch/stefan/7901150/working/3D mkdir: created directory `/scratch/stefan/7901150/working/3D' We are using corina for 3D embeding debuging info:: /scratch/stefan/7901150/working/protonate/xaaaaar_worked-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' 485 3D conformations generated for 448 compounds Building REAL300025567507 mkdir: created directory `/scratch/stefan/7901150/working/building' mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567507' /scratch/stefan/7901150/working/building/REAL300025567507 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567507 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567507/0 /scratch/stefan/7901150/working/building/REAL300025567507 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 1) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/1 `/scratch/stefan/7901150/working/3D/1' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=CC(CS(=O)(=O)NCCC2=NC(=O)O[N-]2)=C1) `REAL300025567507.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567507.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567507/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567507 none N#CC1=CC=CC(CS(=O)(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 1, 1, 1, 1, 1, 5, 14, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 1, 6, 16, 16, 16, 42, 94, 109, 201, 201, 201, 201, 201, 1, 1, 1, 1, 6, 6, 42, 94, 94, 109, 109, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 20, 21, 22, 23, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 634 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567507 none N#CC1=CC=CC(CS(=O)(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 1, 1, 1, 1, 1, 5, 14, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 119, 89, 60, 89, 89, 18, 7, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 119, 119, 60, 19, 19, 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]) total number of confs: 670 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567507 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567507 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 mkdir: created directory `/scratch/stefan/7901150/finished' Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567507/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567507 Building REAL300025567508 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567508' /scratch/stefan/7901150/working/building/REAL300025567508 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567508 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567508/0 /scratch/stefan/7901150/working/building/REAL300025567508 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 2) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/2 `/scratch/stefan/7901150/working/3D/2' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1C) `REAL300025567508.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567508.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567508/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567508 none COCCOC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [5, 12, 5, 5, 12, 1, 1, 1, 1, 14, 11, 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, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 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: [51, 33, 20, 5, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 18, 29, 78, 78, 78, 78, 78, 1, 1, 1, 51, 51, 51, 33, 33, 20, 20, 1, 1, 7, 18, 18, 29, 29, 1, 2, 2, 2] 201 rigid atoms, others: [32, 4, 5, 6, 7, 8, 9, 21, 22, 23, 38, 31] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 39, 40, 41]) total number of confs: 363 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567508 none COCCOC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [5, 12, 5, 5, 12, 1, 1, 1, 1, 14, 11, 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, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 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, 172, 135, 57, 57, 78, 78, 57, 47, 57, 57, 13, 8, 1, 1, 1, 1, 1, 1, 1, 78, 78, 78, 201, 201, 201, 201, 201, 172, 172, 78, 78, 47, 13, 13, 8, 8, 78, 78, 78, 78] 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: 731 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567508 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567508 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567508/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567508 Building REAL300025567509 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567509' /scratch/stefan/7901150/working/building/REAL300025567509 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567509 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567509/0 /scratch/stefan/7901150/working/building/REAL300025567509 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 3) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/3 `/scratch/stefan/7901150/working/3D/3' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1CCN(S(=O)(=O)NCCC2=NC(=O)O[N-]2)CC1) `REAL300025567509.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567509.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567509/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567509 none COC(=O)C1CCN(S(=O)(=O)NCCC2=NC(=O)O[N-]2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 8, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 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, 5, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 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, 3, 1, 3, 1, 1, 1, 1, 1, 6, 6, 6, 17, 50, 60, 113, 113, 113, 113, 113, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 17, 50, 50, 60, 60, 1, 1, 1, 1] 201 rigid atoms, others: [2, 35, 4, 5, 6, 7, 8, 38, 37, 20, 21, 25, 26, 27, 28, 29, 36] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 30, 31, 32, 33, 34]) total number of confs: 365 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567509 none COC(=O)C1CCN(S(=O)(=O)NCCC2=NC(=O)O[N-]2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 8, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 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, 5, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 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, 113, 201, 113, 113, 113, 87, 56, 87, 87, 18, 8, 1, 1, 1, 1, 1, 1, 1, 113, 113, 201, 201, 201, 113, 113, 113, 113, 113, 56, 18, 18, 8, 8, 113, 113, 113, 113] 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: 703 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567509 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567509 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567509/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567509 Building REAL300025567510 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567510' /scratch/stefan/7901150/working/building/REAL300025567510 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567510 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567510/0 /scratch/stefan/7901150/working/building/REAL300025567510 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 4) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/4 `/scratch/stefan/7901150/working/3D/4' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2=CC=C3C(=C2)CC2=CC=CC=C23)[N-]O1) `REAL300025567510.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567510.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567510/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567510 none O=C1N=C(CCNS(=O)(=O)C2=CC=C3C(=C2)CC2=CC=CC=C23)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 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, 1, 9, 25, 77, 109, 109, 109, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 9, 9, 25, 25, 77, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 23, 24] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 608 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567510 none O=C1N=C(CCNS(=O)(=O)C2=CC=C3C(=C2)CC2=CC=CC=C23)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 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: [201, 201, 201, 103, 57, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 103, 103, 57, 57, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31, 32, 33, 34, 35, 36, 37, 38] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 608 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567510 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567510 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567510/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567510 Building REAL300025567511 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567511' /scratch/stefan/7901150/working/building/REAL300025567511 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567511 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567511/0 /scratch/stefan/7901150/working/building/REAL300025567511 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 5) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/5 `/scratch/stefan/7901150/working/3D/5' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1) `REAL300025567511.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567511.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567511/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567511 none CC(C)CC1=CC=C(S(=O)(=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', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 1, 1, 1, 1, 14, 11, 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, 6, 6, 4, 7, 7, 7, 7, 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, 3, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 45, 81, 185, 185, 185, 185, 185, 1, 1, 4, 4, 4, 4, 4, 4, 4, 3, 3, 1, 1, 9, 45, 45, 81, 81, 1, 1] 201 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 39, 20, 21, 38, 31] set([0, 1, 2, 9, 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: 530 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567511 none CC(C)CC1=CC=C(S(=O)(=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', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 1, 1, 1, 1, 14, 11, 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, 6, 6, 4, 7, 7, 7, 7, 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, 191, 201, 185, 178, 185, 185, 109, 73, 109, 109, 22, 8, 1, 1, 1, 1, 1, 1, 1, 185, 185, 201, 201, 201, 201, 201, 201, 201, 191, 191, 185, 185, 73, 23, 23, 8, 8, 185, 185] 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: 712 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567511 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567511 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567511/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567511 Building REAL300025567512 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567512' /scratch/stefan/7901150/working/building/REAL300025567512 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567512 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567512/0 /scratch/stefan/7901150/working/building/REAL300025567512 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 6) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/6 `/scratch/stefan/7901150/working/3D/6' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2=C(Cl)C=C3NC(=O)COC3=C2)[N-]O1) `REAL300025567512.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567512.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567512/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567512 none O=C1N=C(CCNS(=O)(=O)C2=C(Cl)C=C3NC(=O)COC3=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', '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, 1, 5, 5, 8, 14, 11, 11, 1, 1, 16, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 12, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 3, 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, 9, 25, 86, 122, 122, 122, 125, 125, 125, 125, 125, 125, 125, 125, 125, 125, 125, 1, 1, 9, 9, 25, 25, 86, 125, 125, 125, 125, 125] 125 rigid atoms, others: [0, 1, 2, 3, 4, 22, 23] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 469 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567512 none O=C1N=C(CCNS(=O)(=O)C2=C(Cl)C=C3NC(=O)COC3=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', '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, 1, 5, 5, 8, 14, 11, 11, 1, 1, 16, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 12, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 125 conformations in input total number of sets (complete confs): 125 using faster count positions algorithm for large data unique positions, atoms: [125, 125, 125, 57, 38, 10, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 125, 125, 57, 57, 38, 38, 10, 1, 1, 1, 1, 1] 125 rigid atoms, others: [32, 33, 7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 354 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567512 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567512 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567512/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567512 Building REAL300025567513 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567513' /scratch/stefan/7901150/working/building/REAL300025567513 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567513 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567513/0 /scratch/stefan/7901150/working/building/REAL300025567513 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 7) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/7 `/scratch/stefan/7901150/working/3D/7' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2=CC=C(Cl)C(Cl)=C2)[N-]O1) `REAL300025567513.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567513.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567513/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567513 none O=C1N=C(CCNS(=O)(=O)C2=CC=C(Cl)C(Cl)=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 16, 1, 16, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 9, 25, 82, 116, 116, 116, 201, 201, 201, 201, 201, 201, 201, 1, 1, 9, 9, 25, 25, 82, 201, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 18, 19] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 630 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567513 none O=C1N=C(CCNS(=O)(=O)C2=CC=C(Cl)C(Cl)=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 16, 1, 16, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 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: [201, 201, 201, 91, 51, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 91, 91, 51, 51, 9, 1, 1, 1] 201 rigid atoms, others: [7, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 566 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567513 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567513 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567513/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567513 Building REAL300025567514 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567514' /scratch/stefan/7901150/working/building/REAL300025567514 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567514 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567514/0 /scratch/stefan/7901150/working/building/REAL300025567514 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 8) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/8 `/scratch/stefan/7901150/working/3D/8' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2=CC=C(Cl)C(C(F)(F)F)=C2)[N-]O1) `REAL300025567514.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567514.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567514/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567514 none O=C1N=C(CCNS(=O)(=O)C2=CC=C(Cl)C(C(F)(F)F)=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 16, 1, 5, 15, 15, 15, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 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 201 conformations in 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, 25, 80, 116, 116, 116, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 9, 9, 25, 25, 80, 201, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 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]) total number of confs: 624 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567514 none O=C1N=C(CCNS(=O)(=O)C2=CC=C(Cl)C(C(F)(F)F)=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 16, 1, 5, 15, 15, 15, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 91, 57, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 201, 201, 91, 91, 57, 57, 9, 1, 1, 1] 201 rigid atoms, others: [7, 10, 11, 12, 13, 14, 15, 16, 20, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 569 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567514 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567514 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567514/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567514 Building REAL300025567515 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567515' /scratch/stefan/7901150/working/building/REAL300025567515 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567515 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567515/0 /scratch/stefan/7901150/working/building/REAL300025567515 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 9) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/9 `/scratch/stefan/7901150/working/3D/9' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)C1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1) `REAL300025567515.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567515.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567515/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567515 none CCC(C)C1=CC=C(S(=O)(=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', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 1, 1, 1, 1, 14, 11, 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, 6, 6, 4, 7, 7, 7, 7, 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, 2, 1, 2, 1, 1, 1, 1, 1, 2, 2, 2, 9, 37, 68, 164, 164, 164, 164, 164, 1, 1, 3, 3, 3, 3, 3, 2, 2, 2, 2, 1, 1, 9, 37, 37, 68, 68, 1, 1] 201 rigid atoms, others: [32, 2, 4, 5, 6, 7, 8, 39, 20, 21, 38, 31] set([0, 1, 3, 9, 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: 456 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567515 none CCC(C)C1=CC=C(S(=O)(=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', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 1, 1, 1, 1, 14, 11, 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, 6, 6, 4, 7, 7, 7, 7, 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, 164, 164, 164, 164, 164, 164, 101, 67, 101, 101, 22, 8, 1, 1, 1, 1, 1, 1, 1, 164, 164, 201, 201, 201, 201, 201, 164, 164, 164, 164, 164, 164, 67, 22, 22, 8, 8, 164, 164] 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: 747 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567515 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567515 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567515/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567515 Building REAL300025567516 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567516' /scratch/stefan/7901150/working/building/REAL300025567516 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567516 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567516/0 /scratch/stefan/7901150/working/building/REAL300025567516 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 10) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/10 `/scratch/stefan/7901150/working/3D/10' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C)C(C)=C1S(=O)(=O)NCCC1=NC(=O)O[N-]1) `REAL300025567516.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567516.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567516/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567516 none CC1=NN(C)C(C)=C1S(=O)(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', '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, 8, 5, 1, 5, 1, 14, 11, 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, 6, 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, 8, 8, 8, 16, 65, 98, 201, 201, 201, 201, 201, 2, 2, 2, 2, 2, 2, 2, 2, 2, 16, 65, 65, 98, 98] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 621 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567516 none CC1=NN(C)C(C)=C1S(=O)(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', '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, 8, 5, 1, 5, 1, 14, 11, 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, 6, 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, 169, 92, 169, 169, 24, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 92, 24, 25, 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]) total number of confs: 715 number of broken/clashed sets: 9 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567516 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567516 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567516/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567516 Building REAL300025567517 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567517' /scratch/stefan/7901150/working/building/REAL300025567517 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567517 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567517/0 /scratch/stefan/7901150/working/building/REAL300025567517 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 11) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/11 `/scratch/stefan/7901150/working/3D/11' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2=CC=CC(Cl)=C2)[N-]O1) `REAL300025567517.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567517.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567517/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567517 none O=C1N=C(CCNS(=O)(=O)C2=CC=CC(Cl)=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 16, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 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: [1, 1, 1, 1, 1, 9, 25, 82, 125, 125, 125, 201, 201, 201, 201, 201, 201, 1, 1, 9, 9, 25, 25, 82, 201, 201, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 17, 18] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 664 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567517 none O=C1N=C(CCNS(=O)(=O)C2=CC=CC(Cl)=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 16, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 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: [201, 201, 201, 89, 52, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 201, 201, 89, 89, 52, 52, 9, 1, 1, 1, 1] 201 rigid atoms, others: [7, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 17, 18, 19, 20, 21, 22, 23]) total number of confs: 559 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567517 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567517 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567517/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567517 Building REAL300025567518 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567518' /scratch/stefan/7901150/working/building/REAL300025567518 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567518 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567518/0 /scratch/stefan/7901150/working/building/REAL300025567518 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 12) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/12 `/scratch/stefan/7901150/working/3D/12' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1) `REAL300025567518.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567518.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567518/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567518 none COC(=O)C1=CC=C(S(=O)(=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', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 11, 1, 1, 1, 1, 14, 11, 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, 3, 7, 5, 7, 7, 7, 7, 7, 6, 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, 5, 1, 5, 1, 1, 1, 1, 1, 2, 2, 2, 9, 47, 84, 200, 200, 200, 200, 200, 1, 1, 6, 6, 6, 1, 1, 9, 47, 47, 84, 84, 1, 1] 201 rigid atoms, others: [32, 33, 2, 4, 5, 6, 7, 8, 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]) total number of confs: 563 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567518 none COC(=O)C1=CC=C(S(=O)(=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', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 11, 1, 1, 1, 1, 14, 11, 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, 3, 7, 5, 7, 7, 7, 7, 7, 6, 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, 200, 201, 125, 200, 200, 125, 89, 125, 125, 24, 8, 1, 1, 1, 1, 1, 1, 1, 200, 200, 201, 201, 201, 200, 200, 89, 25, 25, 8, 8, 200, 200] 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: 1000 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567518 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567518 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567518/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567518 Building REAL300025567519 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567519' /scratch/stefan/7901150/working/building/REAL300025567519 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567519 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567519/0 /scratch/stefan/7901150/working/building/REAL300025567519 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 13) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/13 `/scratch/stefan/7901150/working/3D/13' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C(C)(C)C)C=C1S(=O)(=O)NCCC1=NC(=O)O[N-]1) `REAL300025567519.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567519.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567519/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567519 none CC1=CC=C(C(C)(C)C)C=C1S(=O)(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', '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, 1, 1, 1, 5, 5, 5, 5, 1, 1, 14, 11, 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, 6, 4, 7, 7, 7, 7, 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, 1, 1, 1, 5, 5, 5, 7, 31, 45, 108, 108, 108, 108, 108, 2, 2, 2, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 7, 31, 31, 45, 45] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 9, 10, 11, 26, 27, 37] set([6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42]) total number of confs: 311 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567519 none CC1=CC=C(C(C)(C)C)C=C1S(=O)(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', '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, 1, 1, 1, 5, 5, 5, 5, 1, 1, 14, 11, 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, 6, 4, 7, 7, 7, 7, 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: [108, 108, 108, 97, 108, 108, 201, 201, 201, 108, 97, 66, 97, 97, 24, 8, 1, 1, 1, 1, 1, 1, 1, 108, 108, 108, 108, 97, 201, 201, 201, 201, 201, 201, 201, 201, 201, 108, 66, 24, 24, 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]) total number of confs: 1006 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567519 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567519 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567519/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567519 Building REAL300025567520 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567520' /scratch/stefan/7901150/working/building/REAL300025567520 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567520 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567520/0 /scratch/stefan/7901150/working/building/REAL300025567520 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 14) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/14 `/scratch/stefan/7901150/working/3D/14' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C(CS(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1) `REAL300025567520.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567520.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567520/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567520 none COC(=O)C1=CC=C(CS(=O)(=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', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 14, 11, 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, 6, 4, 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, 5, 1, 5, 1, 1, 1, 1, 1, 6, 22, 22, 22, 48, 98, 98, 197, 197, 197, 197, 197, 1, 1, 6, 6, 6, 1, 1, 6, 6, 48, 98, 98, 98, 98, 1, 1] 201 rigid atoms, others: [2, 35, 4, 5, 6, 7, 8, 21, 22, 36, 26, 27] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 563 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567520 none COC(=O)C1=CC=C(CS(=O)(=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', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 14, 11, 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, 6, 4, 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, 197, 201, 193, 197, 197, 137, 74, 40, 74, 74, 8, 8, 1, 1, 1, 1, 1, 1, 1, 197, 197, 201, 201, 201, 197, 197, 137, 137, 40, 8, 8, 8, 8, 197, 197] 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: 737 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567520 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567520 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567520/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567520 Building REAL300025567521 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567521' /scratch/stefan/7901150/working/building/REAL300025567521 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567521 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567521/0 /scratch/stefan/7901150/working/building/REAL300025567521 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 15) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/15 `/scratch/stefan/7901150/working/3D/15' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2=CC=C3NC(=O)OC3=C2)[N-]O1) `REAL300025567521.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567521.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567521/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567521 none O=C1N=C(CCNS(=O)(=O)C2=CC=C3NC(=O)OC3=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.3', 'C.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 11, 12, 1, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 6, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 6, 3, 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: [1, 1, 1, 1, 1, 9, 25, 87, 129, 129, 129, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 9, 9, 25, 25, 87, 201, 201, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 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]) total number of confs: 653 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567521 none O=C1N=C(CCNS(=O)(=O)C2=CC=C3NC(=O)OC3=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.3', 'C.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 11, 12, 1, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 6, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 6, 3, 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: [201, 201, 201, 87, 54, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 87, 87, 54, 54, 9, 1, 1, 1, 1] 201 rigid atoms, others: [7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 547 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567521 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567521 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567521/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567521 Building REAL300025567522 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567522' /scratch/stefan/7901150/working/building/REAL300025567522 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567522 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567522/0 /scratch/stefan/7901150/working/building/REAL300025567522 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 16) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/16 `/scratch/stefan/7901150/working/3D/16' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1C2=CC=C(S(=O)(=O)NCCC3=NC(=O)O[N-]3)C=C2CC1C) `REAL300025567522.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567522.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567522/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567522 none CC(=O)N1C2=CC=C(S(=O)(=O)NCCC3=NC(=O)O[N-]3)C=C2CC1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 2, 9, 56, 96, 200, 200, 200, 200, 200, 1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 9, 56, 56, 96, 96, 1, 1, 1, 1, 2, 2, 2] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 35, 20, 21, 22, 23, 24, 36, 38, 28, 29, 37] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 30, 31, 32, 33, 34, 39, 40, 41]) total number of confs: 590 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567522 none CC(=O)N1C2=CC=C(S(=O)(=O)NCCC3=NC(=O)O[N-]3)C=C2CC1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 200, 201, 200, 200, 200, 200, 118, 83, 118, 118, 24, 8, 1, 1, 1, 1, 1, 1, 1, 200, 200, 200, 200, 200, 201, 201, 201, 200, 200, 83, 24, 25, 8, 8, 200, 200, 200, 200, 200, 200, 200] 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]) total number of confs: 624 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567522 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567522 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567522/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567522 Building REAL300025567523 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567523' /scratch/stefan/7901150/working/building/REAL300025567523 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025567523 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567523/0 /scratch/stefan/7901150/working/building/REAL300025567523 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 17) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/17 `/scratch/stefan/7901150/working/3D/17' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C1=CNN=C1S(=O)(=O)NCCC1=NC(=O)O[N-]1) `REAL300025567523.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567523.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567523/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567523 none CCOC(=O)C1=CNN=C1S(=O)(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', '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, 5, 12, 1, 11, 1, 1, 8, 8, 1, 14, 11, 11, 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: [7, 7, 3, 7, 5, 7, 7, 4, 7, 7, 7, 6, 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, 1, 7, 7, 7, 13, 42, 65, 160, 160, 160, 160, 160, 18, 18, 18, 18, 18, 1, 1, 13, 42, 42, 65, 65] 201 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 27, 28] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33]) total number of confs: 493 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567523 none CCOC(=O)C1=CNN=C1S(=O)(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', '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, 5, 12, 1, 11, 1, 1, 8, 8, 1, 14, 11, 11, 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: [7, 7, 3, 7, 5, 7, 7, 4, 7, 7, 7, 6, 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, 193, 193, 160, 193, 160, 160, 160, 160, 103, 55, 103, 103, 16, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 160, 160, 55, 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]) total number of confs: 685 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567523 /scratch/stefan/7901150/working /scratch/stefan/7901150 mkdir: created directory `1' /scratch/stefan/7901150/working/building/REAL300025567523/1 /scratch/stefan/7901150/working/building/REAL300025567523 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 1 (index: 18) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/18 `/scratch/stefan/7901150/working/3D/18' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C1=CNN=C1S(=O)(=O)[N-]CCC1=NC(=O)O[N-]1) `REAL300025567523.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025567523.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567523/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567523 none CCOC(=O)C1=CNN=C1S(=O)(=O)[N-]CCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.3', 'C.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, 12, 1, 11, 1, 1, 8, 8, 1, 14, 11, 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, 3, 7, 5, 7, 7, 4, 7, 7, 7, 3, 3, 7, 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: [42, 17, 9, 1, 9, 1, 1, 1, 1, 1, 1, 9, 9, 9, 22, 49, 49, 149, 149, 149, 149, 149, 42, 42, 42, 42, 42, 1, 1, 49, 49, 49, 49] 201 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 27, 28] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32]) total number of confs: 452 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567523 none CCOC(=O)C1=CNN=C1S(=O)(=O)[N-]CCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.3', 'C.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, 12, 1, 11, 1, 1, 8, 8, 1, 14, 11, 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, 3, 7, 5, 7, 7, 4, 7, 7, 7, 3, 3, 7, 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, 184, 180, 149, 180, 149, 149, 149, 149, 66, 26, 66, 66, 8, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 149, 149, 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]) total number of confs: 577 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567523 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567523 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 1: /scratch/stefan/7901150/working/building/REAL300025567523/1.* 0: /scratch/stefan/7901150/working/building/REAL300025567523/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567523 Building REAL300025567524 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567524' /scratch/stefan/7901150/working/building/REAL300025567524 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567524 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567524/0 /scratch/stefan/7901150/working/building/REAL300025567524 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 19) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/19 `/scratch/stefan/7901150/working/3D/19' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C([N+](=O)[O-])=C1) `REAL300025567524.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567524.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567524/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567524 none COC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 12, 1, 1, 1, 1, 14, 11, 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, 3, 7, 7, 7, 7, 7, 6, 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 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, 3, 3, 5, 29, 52, 201, 201, 201, 201, 201, 1, 1, 2, 2, 1, 2, 2, 2, 1, 1, 5, 29, 29, 52, 52, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 33, 18, 19, 22, 26, 27] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 23, 24, 25, 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 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567524 none COC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 12, 1, 1, 1, 1, 14, 11, 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, 3, 7, 7, 7, 7, 7, 6, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 124, 201, 201, 24, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 124, 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: 732 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567524 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567524 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567524/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567524 Building REAL300025567525 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567525' /scratch/stefan/7901150/working/building/REAL300025567525 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567525 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567525/0 /scratch/stefan/7901150/working/building/REAL300025567525 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 20) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/20 `/scratch/stefan/7901150/working/3D/20' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)CC2=CC=C([N+](=O)[O-])C=C2)[N-]O1) `REAL300025567525.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567525.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567525/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567525 none O=C1N=C(CCNS(=O)(=O)CC2=CC=C([N+](=O)[O-])C=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 5, 1, 1, 1, 1, 8, 11, 11, 1, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 3, 3, 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: [1, 1, 1, 1, 1, 9, 25, 92, 131, 131, 131, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 9, 9, 25, 25, 92, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 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, 32]) total number of confs: 839 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567525 none O=C1N=C(CCNS(=O)(=O)CC2=CC=C([N+](=O)[O-])C=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 5, 1, 1, 1, 1, 8, 11, 11, 1, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 3, 3, 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: [201, 201, 201, 120, 95, 35, 11, 3, 11, 11, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 201, 201, 120, 120, 95, 95, 35, 3, 3, 1, 1, 1, 1] 201 rigid atoms, others: [32, 10, 11, 12, 13, 14, 15, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 665 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567525 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567525 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567525/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567525 Building REAL300025567526 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567526' /scratch/stefan/7901150/working/building/REAL300025567526 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567526 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567526/0 /scratch/stefan/7901150/working/building/REAL300025567526 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 21) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/21 `/scratch/stefan/7901150/working/3D/21' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC2=CC=CC(S(=O)(=O)NCCC3=NC(=O)O[N-]3)=C2N=C1) `REAL300025567526.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567526.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567526/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567526 none CC1=CC2=CC=CC(S(=O)(=O)NCCC3=NC(=O)O[N-]3)=C2N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'N.ar', 'C.ar', '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, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 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, 7, 7, 6, 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, 1, 1, 1, 7, 7, 7, 21, 71, 105, 201, 201, 201, 201, 201, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 21, 71, 71, 105, 105, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 35, 20, 21, 22, 26, 27, 28, 29] set([32, 33, 34, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 30, 31]) total number of confs: 634 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567526 none CC1=CC2=CC=CC(S(=O)(=O)NCCC3=NC(=O)O[N-]3)=C2N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'N.ar', 'C.ar', '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, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 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, 7, 7, 6, 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, 201, 201, 201, 155, 81, 155, 155, 20, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 81, 20, 20, 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: 691 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567526 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567526 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567526/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567526 Building REAL300025567527 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567527' /scratch/stefan/7901150/working/building/REAL300025567527 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567527 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567527/0 /scratch/stefan/7901150/working/building/REAL300025567527 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 22) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/22 `/scratch/stefan/7901150/working/3D/22' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1) `REAL300025567527.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567527.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567527/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567527 none CCCOC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 12, 1, 1, 1, 1, 14, 11, 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, 6, 6, 4, 7, 7, 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, 5, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 27, 41, 128, 128, 128, 128, 128, 1, 1, 10, 10, 10, 9, 9, 5, 5, 1, 1, 9, 27, 27, 41, 41, 1, 1] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 20, 21, 36, 29, 30, 37] set([0, 1, 2, 9, 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: 349 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567527 none CCCOC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 12, 1, 1, 1, 1, 14, 11, 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, 6, 6, 4, 7, 7, 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, 191, 128, 78, 128, 128, 78, 60, 78, 78, 16, 8, 1, 1, 1, 1, 1, 1, 1, 128, 128, 201, 201, 201, 201, 201, 201, 201, 128, 128, 60, 17, 17, 8, 8, 128, 128] 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: 827 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567527 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567527 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567527/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567527 Building REAL300025567528 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567528' /scratch/stefan/7901150/working/building/REAL300025567528 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567528 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567528/0 /scratch/stefan/7901150/working/building/REAL300025567528 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 23) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/23 `/scratch/stefan/7901150/working/3D/23' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)CC2=CC=C(F)C=C2)[N-]O1) `REAL300025567528.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567528.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567528/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567528 none O=C1N=C(CCNS(=O)(=O)CC2=CC=C(F)C=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', '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', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 5, 1, 1, 1, 1, 15, 1, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 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: [1, 1, 1, 1, 1, 9, 25, 100, 132, 132, 132, 201, 201, 201, 201, 201, 201, 201, 1, 1, 9, 9, 25, 25, 100, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 18, 19] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 802 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567528 none O=C1N=C(CCNS(=O)(=O)CC2=CC=C(F)C=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', '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', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 5, 1, 1, 1, 1, 15, 1, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 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: [201, 201, 201, 120, 94, 33, 11, 3, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 120, 120, 94, 94, 33, 3, 3, 1, 1, 1, 1] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 660 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567528 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567528 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567528/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567528 Building REAL300025567529 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567529' /scratch/stefan/7901150/working/building/REAL300025567529 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567529 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567529/0 /scratch/stefan/7901150/working/building/REAL300025567529 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 24) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/24 `/scratch/stefan/7901150/working/3D/24' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C(Cl)=C1) `REAL300025567529.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567529.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567529/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567529 none CC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C(Cl)=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.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'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 16, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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 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, 5, 5, 5, 14, 52, 76, 163, 163, 163, 163, 163, 1, 1, 1, 2, 2, 2, 1, 1, 14, 52, 52, 76, 76, 1] 163 rigid atoms, others: [0, 1, 2, 3, 4, 5, 17, 18, 19, 23, 24, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 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 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567529 none CC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C(Cl)=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.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'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 16, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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 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, 150, 92, 150, 150, 21, 8, 1, 1, 1, 1, 1, 1, 1, 163, 163, 163, 163, 163, 163, 163, 163, 92, 21, 21, 8, 8, 163] 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, 27, 28, 29, 30]) total number of confs: 592 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567529 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567529 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567529/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567529 Building REAL300025567530 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567530' /scratch/stefan/7901150/working/building/REAL300025567530 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567530 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567530/0 /scratch/stefan/7901150/working/building/REAL300025567530 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 25) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/25 `/scratch/stefan/7901150/working/3D/25' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2=CC=CC=C2OC(F)(F)F)[N-]O1) `REAL300025567530.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567530.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567530/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567530 none O=C1N=C(CCNS(=O)(=O)C2=CC=CC=C2OC(F)(F)F)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 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: [1, 1, 1, 1, 1, 9, 20, 62, 100, 100, 100, 153, 153, 126, 153, 153, 153, 201, 201, 201, 201, 1, 1, 9, 9, 20, 20, 62, 153, 153, 153, 153] 201 rigid atoms, others: [0, 1, 2, 3, 4, 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]) total number of confs: 708 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567530 none O=C1N=C(CCNS(=O)(=O)C2=CC=CC=C2OC(F)(F)F)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 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: [153, 153, 153, 69, 50, 17, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 5, 11, 11, 11, 153, 153, 69, 69, 50, 50, 17, 1, 1, 1, 1] 201 rigid atoms, others: [7, 10, 11, 12, 13, 14, 15, 16, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 466 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567530 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567530 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567530/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567530 Building REAL300025567531 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567531' /scratch/stefan/7901150/working/building/REAL300025567531 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567531 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567531/0 /scratch/stefan/7901150/working/building/REAL300025567531 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 26) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/26 `/scratch/stefan/7901150/working/3D/26' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=C1) `REAL300025567531.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567531.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567531/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567531 none COC(=O)C1=CC=CC(S(=O)(=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', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 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, 6, 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: [6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 39, 63, 121, 121, 121, 121, 121, 1, 7, 7, 7, 1, 1, 1, 9, 39, 39, 63, 63, 1] 201 rigid atoms, others: [33, 2, 4, 5, 6, 7, 8, 9, 21, 25, 26, 27] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 28, 29, 30, 31, 32]) total number of confs: 402 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567531 none COC(=O)C1=CC=CC(S(=O)(=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', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 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, 6, 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, 121, 201, 121, 121, 121, 121, 71, 44, 71, 71, 18, 8, 1, 1, 1, 1, 1, 1, 1, 121, 201, 201, 201, 121, 121, 121, 44, 18, 18, 8, 8, 121] 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: 706 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567531 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567531 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567531/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567531 Building REAL300025567532 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567532' /scratch/stefan/7901150/working/building/REAL300025567532 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567532 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567532/0 /scratch/stefan/7901150/working/building/REAL300025567532 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 27) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/27 `/scratch/stefan/7901150/working/3D/27' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C(=O)C2=CC=C(S(=O)(=O)NCCC3=NC(=O)O[N-]3)C=C2C1=O) `REAL300025567532.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567532.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567532/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567532 none CN1C(=O)C2=CC=C(S(=O)(=O)NCCC3=NC(=O)O[N-]3)C=C2C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 54, 88, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 54, 54, 88, 88, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 34, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([32, 33, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31]) total number of confs: 549 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567532 none CN1C(=O)C2=CC=C(S(=O)(=O)NCCC3=NC(=O)O[N-]3)C=C2C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 132, 91, 132, 132, 24, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 91, 24, 24, 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]) total number of confs: 651 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567532 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567532 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567532/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567532 Building REAL300025567533 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567533' /scratch/stefan/7901150/working/building/REAL300025567533 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567533 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567533/0 /scratch/stefan/7901150/working/building/REAL300025567533 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 28) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/28 `/scratch/stefan/7901150/working/3D/28' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2=CC=C3OCC(=O)NC3=C2)[N-]O1) `REAL300025567533.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567533.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567533/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567533 none O=C1N=C(CCNS(=O)(=O)C2=CC=C3OCC(=O)NC3=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 1, 11, 8, 1, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 6, 4, 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: [1, 1, 1, 1, 1, 9, 25, 85, 123, 123, 123, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 9, 9, 25, 25, 85, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 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]) total number of confs: 633 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567533 none O=C1N=C(CCNS(=O)(=O)C2=CC=C3OCC(=O)NC3=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 1, 11, 8, 1, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 6, 4, 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: [201, 201, 201, 90, 56, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 90, 90, 56, 56, 9, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 561 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567533 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567533 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567533/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567533 Building REAL300025567534 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567534' /scratch/stefan/7901150/working/building/REAL300025567534 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567534 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567534/0 /scratch/stefan/7901150/working/building/REAL300025567534 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 29) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/29 `/scratch/stefan/7901150/working/3D/29' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NS(=O)(=O)C1=CC=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=C1) `REAL300025567534.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567534/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567534 none NS(=O)(=O)C1=CC=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.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, 14, 11, 11, 1, 1, 1, 1, 1, 14, 11, 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, 6, 6, 7, 7, 7, 7, 7, 7, 6, 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: [4, 1, 4, 4, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 42, 58, 140, 140, 140, 140, 140, 1, 5, 5, 1, 1, 1, 9, 42, 42, 58, 58, 1] 201 rigid atoms, others: [32, 1, 4, 5, 6, 7, 8, 9, 21, 24, 25, 26] set([0, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 27, 28, 29, 30, 31]) total number of confs: 391 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567534 none NS(=O)(=O)C1=CC=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.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, 14, 11, 11, 1, 1, 1, 1, 1, 14, 11, 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, 6, 6, 7, 7, 7, 7, 7, 7, 6, 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, 140, 201, 201, 140, 140, 140, 140, 100, 73, 100, 100, 24, 8, 1, 1, 1, 1, 1, 1, 1, 140, 201, 201, 140, 140, 140, 73, 24, 24, 8, 8, 140] 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: 783 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567534 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567534 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567534/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567534 Building REAL300025567535 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567535' /scratch/stefan/7901150/working/building/REAL300025567535 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567535 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567535/0 /scratch/stefan/7901150/working/building/REAL300025567535 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 30) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/30 `/scratch/stefan/7901150/working/3D/30' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2=CC=CN=C2Cl)[N-]O1) `REAL300025567535.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567535.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567535/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567535 none O=C1N=C(CCNS(=O)(=O)C2=CC=CN=C2Cl)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 16, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 183 conformations in input total number of sets (complete confs): 183 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 9, 25, 97, 161, 161, 161, 183, 183, 183, 183, 183, 183, 1, 1, 9, 9, 25, 25, 97, 183, 183, 183] 183 rigid atoms, others: [0, 1, 2, 3, 4, 17, 18] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 656 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567535 none O=C1N=C(CCNS(=O)(=O)C2=CC=CN=C2Cl)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 16, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 183 conformations in input total number of sets (complete confs): 183 using faster count positions algorithm for large data unique positions, atoms: [183, 183, 183, 89, 59, 19, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 183, 183, 89, 89, 59, 59, 19, 1, 1, 1] 183 rigid atoms, others: [7, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 17, 18, 19, 20, 21, 22, 23]) total number of confs: 526 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567535 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567535 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567535/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567535 Building REAL300025567536 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567536' /scratch/stefan/7901150/working/building/REAL300025567536 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567536 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567536/0 /scratch/stefan/7901150/working/building/REAL300025567536 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 31) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/31 `/scratch/stefan/7901150/working/3D/31' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C(=O)CC2=CC(S(=O)(=O)NCCC3=NC(=O)O[N-]3)=CC=C21) `REAL300025567536.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567536.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567536/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567536 none CN1C(=O)CC2=CC(S(=O)(=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.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 8, 1, 11, 5, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 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, 6, 6, 4, 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, 2, 2, 2, 9, 52, 90, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 52, 52, 90, 90, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 34, 35, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([32, 33, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31]) total number of confs: 563 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567536 none CN1C(=O)CC2=CC(S(=O)(=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.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 8, 1, 11, 5, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 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, 6, 6, 4, 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, 112, 80, 112, 112, 24, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 80, 24, 24, 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: 615 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567536 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567536 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567536/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567536 Building REAL300025567537 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567537' /scratch/stefan/7901150/working/building/REAL300025567537 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567537 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567537/0 /scratch/stefan/7901150/working/building/REAL300025567537 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 32) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/32 `/scratch/stefan/7901150/working/3D/32' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2=CC=C3NC(=O)C(=O)NC3=C2)[N-]O1) `REAL300025567537.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567537.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567537/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567537 none O=C1N=C(CCNS(=O)(=O)C2=CC=C3NC(=O)C(=O)NC3=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', '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, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 11, 1, 11, 8, 1, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 6, 7, 6, 4, 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: [1, 1, 1, 1, 1, 9, 25, 86, 121, 121, 121, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 9, 9, 25, 25, 86, 201, 201, 201, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 22, 23] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 624 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567537 none O=C1N=C(CCNS(=O)(=O)C2=CC=C3NC(=O)C(=O)NC3=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', '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, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 11, 1, 11, 8, 1, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 6, 7, 6, 4, 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: [201, 201, 201, 91, 55, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 91, 91, 55, 55, 9, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 564 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567537 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567537 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567537/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567537 Building REAL300025567538 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567538' /scratch/stefan/7901150/working/building/REAL300025567538 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567538 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567538/0 /scratch/stefan/7901150/working/building/REAL300025567538 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 33) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/33 `/scratch/stefan/7901150/working/3D/33' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)C1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1) `REAL300025567538.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567538.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567538/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567538 none CS(=O)(=O)C1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 14, 11, 11, 1, 1, 1, 1, 14, 11, 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, 3, 3, 7, 7, 7, 7, 7, 6, 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 170 conformations in input total number of sets (complete confs): 170 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 1, 1, 2, 2, 2, 9, 43, 73, 170, 170, 170, 170, 170, 1, 1, 2, 2, 2, 1, 1, 9, 43, 43, 73, 73, 1, 1] 170 rigid atoms, others: [32, 1, 33, 4, 5, 6, 7, 8, 20, 21, 25, 26] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 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 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567538 none CS(=O)(=O)C1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 14, 11, 11, 1, 1, 1, 1, 14, 11, 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, 3, 3, 7, 7, 7, 7, 7, 6, 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 170 conformations in input total number of sets (complete confs): 170 using faster count positions algorithm for large data unique positions, atoms: [170, 135, 170, 170, 135, 170, 170, 135, 92, 135, 135, 24, 8, 1, 1, 1, 1, 1, 1, 1, 170, 170, 170, 170, 170, 170, 170, 92, 25, 25, 8, 8, 170, 170] 170 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: 904 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567538 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567538 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567538/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567538 Building REAL300025567539 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567539' /scratch/stefan/7901150/working/building/REAL300025567539 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567539 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567539/0 /scratch/stefan/7901150/working/building/REAL300025567539 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 34) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/34 `/scratch/stefan/7901150/working/3D/34' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)N2CCC3=CC=CC=C3C2)[N-]O1) `REAL300025567539.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567539.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567539/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567539 none O=C1N=C(CCNS(=O)(=O)N2CCC3=CC=CC=C3C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 5, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 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, 1, 1, 9, 21, 84, 143, 143, 143, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 9, 9, 21, 21, 84, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 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, 32, 33, 34, 35, 36]) total number of confs: 639 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567539 none O=C1N=C(CCNS(=O)(=O)N2CCC3=CC=CC=C3C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 5, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 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: [201, 201, 201, 108, 75, 20, 6, 1, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 108, 108, 75, 75, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 640 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567539 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567539 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567539/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567539 Building REAL300025567540 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567540' /scratch/stefan/7901150/working/building/REAL300025567540 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567540 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567540/0 /scratch/stefan/7901150/working/building/REAL300025567540 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 35) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/35 `/scratch/stefan/7901150/working/3D/35' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2=CC=C3OC(=O)C=CC3=C2)[N-]O1) `REAL300025567540.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567540.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567540/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567540 none O=C1N=C(CCNS(=O)(=O)C2=CC=C3OC(=O)C=CC3=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', '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, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 5, 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: [1, 1, 1, 1, 1, 9, 25, 86, 123, 123, 123, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 9, 9, 25, 25, 86, 201, 201, 201, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 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]) total number of confs: 635 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567540 none O=C1N=C(CCNS(=O)(=O)C2=CC=C3OC(=O)C=CC3=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', '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, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 5, 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: [201, 201, 201, 93, 56, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 93, 93, 56, 56, 9, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 567 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567540 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567540 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567540/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567540 Building REAL300025567541 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567541' /scratch/stefan/7901150/working/building/REAL300025567541 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567541 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567541/0 /scratch/stefan/7901150/working/building/REAL300025567541 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 36) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/36 `/scratch/stefan/7901150/working/3D/36' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2=CC=CC(OC(F)(F)F)=C2)[N-]O1) `REAL300025567541.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567541.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567541/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567541 none O=C1N=C(CCNS(=O)(=O)C2=CC=CC(OC(F)(F)F)=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 8, 12, 43, 49, 49, 49, 76, 76, 76, 76, 76, 201, 201, 201, 201, 76, 1, 1, 8, 8, 12, 12, 43, 76, 76, 76, 76] 201 rigid atoms, others: [0, 1, 2, 3, 4, 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]) total number of confs: 401 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567541 none O=C1N=C(CCNS(=O)(=O)C2=CC=CC(OC(F)(F)F)=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 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: [76, 76, 76, 30, 18, 7, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 8, 10, 10, 10, 1, 76, 76, 30, 30, 18, 18, 7, 1, 1, 1, 1] 201 rigid atoms, others: [7, 10, 11, 12, 13, 14, 15, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 228 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567541 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567541 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567541/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567541 Building REAL300025567542 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567542' /scratch/stefan/7901150/working/building/REAL300025567542 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567542 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567542/0 /scratch/stefan/7901150/working/building/REAL300025567542 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 37) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/37 `/scratch/stefan/7901150/working/3D/37' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C2=CC=CN=C12) `REAL300025567542.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567542.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567542/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567542 none CC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C2=CC=CN=C12 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.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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 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, 1, 3, 3, 3, 7, 29, 53, 131, 131, 131, 131, 131, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 7, 29, 29, 53, 53, 1, 1, 1] 131 rigid atoms, others: [0, 1, 2, 3, 4, 5, 35, 33, 34, 17, 18, 19, 20, 21, 22, 26, 27] set([32, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 28, 29, 30, 31]) total number of confs: 360 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567542 none CC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C2=CC=CN=C12 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.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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 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, 131, 131, 77, 131, 131, 24, 8, 1, 1, 1, 1, 1, 1, 1, 131, 131, 131, 131, 131, 131, 131, 131, 131, 131, 131, 77, 25, 25, 8, 8, 131, 131, 131] 131 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: 543 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567542 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567542 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567542/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567542 Building REAL300025567543 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567543' /scratch/stefan/7901150/working/building/REAL300025567543 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567543 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567543/0 /scratch/stefan/7901150/working/building/REAL300025567543 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 38) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/38 `/scratch/stefan/7901150/working/3D/38' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C(=O)OC2=CC(S(=O)(=O)NCCC3=NC(=O)O[N-]3)=CC=C21) `REAL300025567543.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567543.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567543/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567543 none CN1C(=O)OC2=CC(S(=O)(=O)NCCC3=NC(=O)O[N-]3)=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [5, 8, 1, 11, 12, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 3, 7, 7, 7, 7, 6, 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, 3, 3, 3, 9, 51, 86, 201, 201, 201, 201, 201, 1, 1, 1, 2, 2, 2, 1, 9, 51, 51, 86, 86, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 33, 20, 21, 22, 26] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 27, 28, 29, 30, 31]) total number of confs: 549 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567543 none CN1C(=O)OC2=CC(S(=O)(=O)NCCC3=NC(=O)O[N-]3)=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [5, 8, 1, 11, 12, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 3, 7, 7, 7, 7, 6, 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, 132, 89, 132, 132, 24, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 89, 24, 24, 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]) total number of confs: 659 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567543 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567543 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567543/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567543 Building REAL300025567544 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567544' /scratch/stefan/7901150/working/building/REAL300025567544 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567544 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567544/0 /scratch/stefan/7901150/working/building/REAL300025567544 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 39) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/39 `/scratch/stefan/7901150/working/3D/39' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2=CC=C3NC(=O)NC(=O)C3=C2)[N-]O1) `REAL300025567544.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567544.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567544/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567544 none O=C1N=C(CCNS(=O)(=O)C2=CC=C3NC(=O)NC(=O)C3=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', '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, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 11, 8, 1, 11, 1, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 6, 4, 7, 6, 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: [1, 1, 1, 1, 1, 9, 25, 90, 131, 131, 131, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 9, 9, 25, 25, 90, 201, 201, 201, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 22, 23] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 640 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567544 none O=C1N=C(CCNS(=O)(=O)C2=CC=C3NC(=O)NC(=O)C3=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', '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, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 11, 8, 1, 11, 1, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 6, 4, 7, 6, 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: [201, 201, 201, 89, 53, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 89, 89, 53, 53, 9, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 549 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567544 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567544 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567544/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567544 Building REAL300025567545 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567545' /scratch/stefan/7901150/working/building/REAL300025567545 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567545 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567545/0 /scratch/stefan/7901150/working/building/REAL300025567545 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 40) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/40 `/scratch/stefan/7901150/working/3D/40' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(F)=CC=C1S(=O)(=O)NCCC1=NC(=O)O[N-]1) `REAL300025567545.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567545.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567545/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567545 none CC1=CC(F)=CC=C1S(=O)(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.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, 15, 1, 1, 1, 14, 11, 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, 6, 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 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, 1, 1, 1, 1, 1, 5, 5, 5, 13, 39, 63, 153, 153, 153, 153, 153, 2, 2, 2, 1, 1, 1, 13, 41, 41, 63, 63] 153 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 23, 24, 25] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567545 none CC1=CC(F)=CC=C1S(=O)(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.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, 15, 1, 1, 1, 14, 11, 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, 6, 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 153 conformations in input total number of sets (complete confs): 153 using faster count positions algorithm for large data unique positions, atoms: [153, 153, 153, 143, 153, 153, 153, 143, 88, 143, 143, 24, 8, 1, 1, 1, 1, 1, 1, 1, 153, 153, 153, 153, 153, 153, 88, 24, 24, 8, 8] 153 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: 627 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567545 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567545 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567545/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567545 Building REAL300025567546 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567546' /scratch/stefan/7901150/working/building/REAL300025567546 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567546 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567546/0 /scratch/stefan/7901150/working/building/REAL300025567546 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 41) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/41 `/scratch/stefan/7901150/working/3D/41' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1=C(F)C=CC=C1Cl)S(=O)(=O)NCCC1=NC(=O)O[N-]1) `REAL300025567546.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567546.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567546/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567546 none CN(CC1=C(F)C=CC=C1Cl)S(=O)(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.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, 5, 1, 1, 15, 1, 1, 1, 1, 16, 14, 11, 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, 6, 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: [17, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 37, 37, 37, 53, 111, 111, 201, 201, 201, 201, 201, 17, 17, 17, 4, 4, 1, 1, 1, 53, 111, 111, 111, 111] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30] set([0, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35]) total number of confs: 631 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567546 none CN(CC1=C(F)C=CC=C1Cl)S(=O)(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.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, 5, 1, 1, 15, 1, 1, 1, 1, 16, 14, 11, 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, 6, 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: [107, 73, 107, 178, 201, 201, 201, 194, 201, 201, 201, 46, 73, 73, 8, 8, 1, 1, 1, 1, 1, 1, 1, 107, 107, 107, 178, 178, 201, 194, 201, 46, 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: 802 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567546 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567546 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567546/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567546 Building REAL300025567547 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567547' /scratch/stefan/7901150/working/building/REAL300025567547 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567547 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567547/0 /scratch/stefan/7901150/working/building/REAL300025567547 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 42) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/42 `/scratch/stefan/7901150/working/3D/42' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2=CC=C(I)C=C2)[N-]O1) `REAL300025567547.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567547.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567547/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567547 none O=C1N=C(CCNS(=O)(=O)C2=CC=C(I)C=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 18, 1, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 9, 25, 92, 136, 136, 136, 136, 136, 136, 136, 136, 136, 1, 1, 9, 9, 25, 25, 92, 136, 136, 136, 136] 136 rigid atoms, others: [0, 1, 2, 3, 4, 17, 18] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 525 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567547 none O=C1N=C(CCNS(=O)(=O)C2=CC=C(I)C=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 18, 1, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 59, 30, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 137, 137, 59, 59, 30, 30, 5, 1, 1, 1, 1] 137 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 17, 18, 19, 20, 21, 22, 23]) total number of confs: 369 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567547 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567547 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567547/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567547 Building REAL300025567548 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567548' /scratch/stefan/7901150/working/building/REAL300025567548 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567548 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567548/0 /scratch/stefan/7901150/working/building/REAL300025567548 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 43) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/43 `/scratch/stefan/7901150/working/3D/43' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNS(=O)(=O)C1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1) `REAL300025567548.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567548.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567548/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567548 none CNS(=O)(=O)C1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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: [5, 8, 14, 11, 11, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 6, 6, 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, 2, 2, 1, 1, 1, 1, 1, 2, 2, 2, 7, 33, 53, 201, 201, 201, 201, 201, 1, 1, 5, 5, 5, 5, 1, 1, 7, 33, 33, 53, 53, 1, 1] 201 rigid atoms, others: [2, 35, 5, 6, 7, 8, 9, 34, 21, 22, 27, 28] set([0, 1, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 29, 30, 31, 32, 33]) total number of confs: 439 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567548 none CNS(=O)(=O)C1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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: [5, 8, 14, 11, 11, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 6, 6, 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, 159, 201, 201, 159, 201, 201, 159, 104, 159, 159, 22, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 104, 23, 23, 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]) total number of confs: 1060 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567548 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567548 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567548/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567548 Building REAL300025567549 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567549' /scratch/stefan/7901150/working/building/REAL300025567549 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567549 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567549/0 /scratch/stefan/7901150/working/building/REAL300025567549 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 44) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/44 `/scratch/stefan/7901150/working/3D/44' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)C1=CC=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=C1) `REAL300025567549.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567549.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567549/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567549 none CS(=O)(=O)C1=CC=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.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'] dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 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, 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, 1, 2, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 47, 67, 169, 169, 169, 169, 169, 1, 3, 3, 3, 1, 1, 1, 9, 47, 47, 67, 67, 1] 201 rigid atoms, others: [1, 33, 4, 5, 6, 7, 8, 9, 21, 25, 26, 27] set([0, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 28, 29, 30, 31, 32]) total number of confs: 456 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567549 none CS(=O)(=O)C1=CC=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.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'] dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 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, 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, 169, 201, 201, 169, 121, 169, 169, 120, 89, 120, 120, 24, 8, 1, 1, 1, 1, 1, 1, 1, 169, 201, 201, 201, 120, 169, 169, 89, 24, 24, 8, 8, 169] 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: 890 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567549 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567549 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567549/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567549 Building REAL300025567550 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567550' /scratch/stefan/7901150/working/building/REAL300025567550 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567550 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567550/0 /scratch/stefan/7901150/working/building/REAL300025567550 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 45) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/45 `/scratch/stefan/7901150/working/3D/45' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2=CC=CC=C2C2=CC=CC=C2)[N-]O1) `REAL300025567550.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567550.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567550/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567550 none O=C1N=C(CCNS(=O)(=O)C2=CC=CC=C2C2=CC=CC=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 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 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, 9, 24, 88, 150, 150, 150, 156, 156, 152, 156, 156, 156, 156, 156, 156, 156, 156, 1, 1, 9, 9, 24, 24, 88, 156, 156, 156, 156, 156, 156, 156, 156, 156] 156 rigid atoms, others: [0, 1, 2, 3, 4, 22, 23] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 631 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567550 none O=C1N=C(CCNS(=O)(=O)C2=CC=CC=C2C2=CC=CC=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 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 156 conformations in input total number of sets (complete confs): 156 using faster count positions algorithm for large data unique positions, atoms: [156, 156, 156, 81, 53, 11, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 2, 2, 156, 156, 81, 81, 53, 53, 11, 1, 1, 1, 1, 2, 2, 2, 2, 2] 156 rigid atoms, others: [32, 7, 10, 11, 12, 13, 14, 15, 16, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37]) 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567550 none O=C1N=C(CCNS(=O)(=O)C2=CC=CC=C2C2=CC=CC=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 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 156 conformations in input total number of sets (complete confs): 156 using faster count positions algorithm for large data unique positions, atoms: [156, 156, 156, 81, 53, 11, 7, 2, 7, 7, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 156, 156, 81, 81, 53, 53, 11, 2, 2, 2, 2, 1, 1, 1, 1, 1] 156 rigid atoms, others: [33, 34, 35, 36, 37, 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: 487 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567550 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567550 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567550/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567550 Building REAL300025567551 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567551' /scratch/stefan/7901150/working/building/REAL300025567551 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567551 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567551/0 /scratch/stefan/7901150/working/building/REAL300025567551 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 46) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/46 `/scratch/stefan/7901150/working/3D/46' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2=CC=C(F)C=C2Cl)[N-]O1) `REAL300025567551.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567551/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567551 none O=C1N=C(CCNS(=O)(=O)C2=CC=C(F)C=C2Cl)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 15, 1, 1, 16, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [1, 1, 1, 1, 1, 9, 22, 94, 152, 152, 152, 164, 164, 164, 164, 164, 164, 164, 1, 1, 9, 9, 22, 22, 94, 164, 164, 164] 164 rigid atoms, others: [0, 1, 2, 3, 4, 18, 19] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 595 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567551 none O=C1N=C(CCNS(=O)(=O)C2=CC=C(F)C=C2Cl)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 15, 1, 1, 16, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 75, 51, 14, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 164, 164, 75, 75, 51, 51, 14, 1, 1, 1] 164 rigid atoms, others: [7, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 462 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567551 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567551 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567551/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567551 Building REAL300025567552 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567552' /scratch/stefan/7901150/working/building/REAL300025567552 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567552 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567552/0 /scratch/stefan/7901150/working/building/REAL300025567552 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 47) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/47 `/scratch/stefan/7901150/working/3D/47' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(C1=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=CN1)N1CCCC1) `REAL300025567552.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567552.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567552/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567552 none O=C(C1=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=CN1)N1CCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.pl3', 'N.am', '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, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 8, 5, 5, 5, 5, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 1, 1, 1, 1, 3, 3, 3, 9, 40, 58, 151, 151, 151, 151, 151, 1, 1, 10, 17, 17, 17, 17, 1, 9, 40, 40, 58, 58, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17] 201 rigid atoms, others: [1, 2, 3, 4, 5, 17, 18, 24, 30, 31] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 425 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567552 none O=C(C1=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=CN1)N1CCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.pl3', 'N.am', '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, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 8, 5, 5, 5, 5, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 151, 151, 151, 109, 74, 109, 109, 20, 8, 1, 1, 1, 1, 1, 1, 1, 151, 151, 201, 201, 201, 201, 201, 151, 74, 20, 20, 8, 8, 151, 151, 201, 201, 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]) total number of confs: 692 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567552 none O=C(C1=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=CN1)N1CCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.pl3', 'N.am', '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, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 8, 5, 5, 5, 5, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need 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, 17, 17, 17, 19, 19, 19, 40, 86, 103, 201, 201, 201, 201, 201, 17, 17, 1, 1, 1, 1, 1, 17, 40, 86, 86, 103, 103, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 1, 34, 35, 36, 37, 38, 33, 39, 19, 20, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 568 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567552 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567552 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567552/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567552 Building REAL300025567553 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567553' /scratch/stefan/7901150/working/building/REAL300025567553 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567553 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567553/0 /scratch/stefan/7901150/working/building/REAL300025567553 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 48) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/48 `/scratch/stefan/7901150/working/3D/48' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C(F)=C1) `REAL300025567553.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567553.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567553/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567553 none CC(=O)NC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 15, 1, 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, 6, 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, 7, 7, 7, 13, 44, 64, 161, 161, 161, 161, 161, 1, 1, 1, 4, 4, 4, 4, 1, 1, 13, 44, 44, 64, 64, 1] 201 rigid atoms, others: [34, 3, 4, 5, 6, 7, 8, 20, 21, 22, 27, 28] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 29, 30, 31, 32, 33]) total number of confs: 438 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567553 none CC(=O)NC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 15, 1, 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, 6, 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, 159, 159, 161, 161, 119, 87, 119, 119, 24, 8, 1, 1, 1, 1, 1, 1, 1, 161, 161, 161, 201, 201, 201, 201, 161, 161, 87, 24, 25, 8, 8, 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]) total number of confs: 698 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567553 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567553 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567553/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567553 Building REAL300025567554 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567554' /scratch/stefan/7901150/working/building/REAL300025567554 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567554 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567554/0 /scratch/stefan/7901150/working/building/REAL300025567554 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 49) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/49 `/scratch/stefan/7901150/working/3D/49' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2=CC3=C(C=C2)OC2=C3C=CC=C2)[N-]O1) `REAL300025567554.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567554/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567554 none O=C1N=C(CCNS(=O)(=O)C2=CC3=C(C=C2)OC2=C3C=CC=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 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] 0 hydrogens need rotated 201 conformations in 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, 25, 94, 147, 147, 147, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 9, 9, 25, 25, 94, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 23, 24] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 676 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567554 none O=C1N=C(CCNS(=O)(=O)C2=CC3=C(C=C2)OC2=C3C=CC=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 93, 55, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 93, 93, 55, 55, 9, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 574 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567554 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567554 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567554/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567554 Building REAL300025567555 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567555' /scratch/stefan/7901150/working/building/REAL300025567555 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567555 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567555/0 /scratch/stefan/7901150/working/building/REAL300025567555 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 50) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/50 `/scratch/stefan/7901150/working/3D/50' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)S(=O)(=O)C1=CC=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=C1) `REAL300025567555.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567555/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567555 none CN(C)S(=O)(=O)C1=CC=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.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, 8, 5, 14, 11, 11, 1, 1, 1, 1, 1, 14, 11, 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, 6, 6, 7, 7, 7, 7, 7, 7, 6, 6, 4, 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, 16, 1, 8, 8, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 36, 50, 119, 119, 119, 119, 119, 1, 16, 16, 16, 17, 17, 17, 1, 1, 1, 9, 36, 36, 50, 50, 1] 201 rigid atoms, others: [32, 3, 38, 6, 7, 8, 9, 10, 11, 23, 30, 31] set([0, 1, 2, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37]) total number of confs: 388 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567555 none CN(C)S(=O)(=O)C1=CC=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.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, 8, 5, 14, 11, 11, 1, 1, 1, 1, 1, 14, 11, 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, 6, 6, 7, 7, 7, 7, 7, 7, 6, 6, 4, 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, 119, 201, 201, 119, 92, 119, 119, 91, 68, 91, 91, 18, 8, 1, 1, 1, 1, 1, 1, 1, 119, 201, 201, 201, 201, 201, 201, 91, 119, 119, 68, 18, 18, 8, 8, 119] 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: 920 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567555 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567555 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567555/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567555 Building REAL300025567556 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567556' /scratch/stefan/7901150/working/building/REAL300025567556 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567556 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567556/0 /scratch/stefan/7901150/working/building/REAL300025567556 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 51) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/51 `/scratch/stefan/7901150/working/3D/51' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC(C)CN(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C1) `REAL300025567556.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567556.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567556/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567556 none CC1CC(C)CN(S(=O)(=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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 5, 5, 8, 14, 11, 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, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 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, 6, 6, 6, 17, 65, 104, 201, 201, 201, 201, 201, 1, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 1, 1, 17, 65, 65, 104, 104, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 19, 23, 24, 25, 26, 38, 37, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 27, 28, 29, 32, 33, 34, 35, 36]) total number of confs: 643 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567556 none CC1CC(C)CN(S(=O)(=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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 5, 5, 8, 14, 11, 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, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 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, 167, 90, 167, 167, 21, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 90, 21, 21, 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]) total number of confs: 701 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567556 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567556 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567556/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567556 Building REAL300025567557 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567557' /scratch/stefan/7901150/working/building/REAL300025567557 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567557 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567557/0 /scratch/stefan/7901150/working/building/REAL300025567557 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 52) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/52 `/scratch/stefan/7901150/working/3D/52' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(F)=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1OC) `REAL300025567557.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567557/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567557 none COC1=CC(F)=C(S(=O)(=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', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 15, 1, 14, 11, 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, 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, 19, 60, 74, 147, 147, 147, 147, 147, 1, 1, 1, 3, 4, 4, 4, 1, 19, 60, 60, 74, 74, 1, 4, 4, 4] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 26] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 27, 28, 29, 30, 31, 33, 34, 35]) total number of confs: 454 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567557 none COC1=CC(F)=C(S(=O)(=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', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 15, 1, 14, 11, 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, 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, 147, 147, 147, 144, 147, 94, 61, 94, 94, 16, 8, 1, 1, 1, 1, 1, 1, 1, 147, 147, 147, 201, 201, 201, 201, 147, 61, 16, 16, 8, 8, 147, 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]) total number of confs: 687 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567557 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567557 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567557/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567557 Building REAL300025567558 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567558' /scratch/stefan/7901150/working/building/REAL300025567558 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567558 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567558/0 /scratch/stefan/7901150/working/building/REAL300025567558 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 53) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/53 `/scratch/stefan/7901150/working/3D/53' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C)=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1OC) `REAL300025567558.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567558.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567558/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567558 none COC1=CC(C)=C(S(=O)(=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', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 12, 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, 6, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 25, 43, 128, 128, 128, 128, 128, 1, 1, 1, 3, 4, 4, 4, 1, 2, 2, 2, 5, 25, 25, 43, 43, 1, 4, 4, 4] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 26, 35] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38]) total number of confs: 330 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567558 none COC1=CC(C)=C(S(=O)(=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', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 12, 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, 6, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 128, 128, 128, 128, 128, 128, 80, 128, 128, 24, 8, 1, 1, 1, 1, 1, 1, 1, 128, 128, 128, 201, 201, 201, 201, 128, 128, 128, 128, 80, 24, 24, 8, 8, 128, 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]) total number of confs: 745 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567558 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567558 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567558/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567558 Building REAL300025567559 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567559' /scratch/stefan/7901150/working/building/REAL300025567559 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567559 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567559/0 /scratch/stefan/7901150/working/building/REAL300025567559 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 54) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/54 `/scratch/stefan/7901150/working/3D/54' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C1CCN(S(=O)(=O)NCCC2=NC(=O)O[N-]2)CC1) `REAL300025567559.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567559.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567559/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567559 none CCOC(=O)C1CCN(S(=O)(=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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 5, 12, 1, 11, 5, 5, 5, 8, 14, 11, 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, 3, 7, 5, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 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: [28, 12, 12, 1, 12, 1, 1, 1, 1, 1, 6, 6, 6, 9, 19, 23, 73, 73, 73, 73, 73, 1, 1, 28, 28, 28, 28, 28, 1, 1, 1, 1, 1, 9, 19, 19, 23, 23, 1, 1, 1, 1] 201 rigid atoms, others: [32, 3, 5, 6, 7, 8, 9, 39, 40, 21, 22, 41, 38, 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, 33, 34, 35, 36, 37]) total number of confs: 268 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567559 none CCOC(=O)C1CCN(S(=O)(=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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 5, 12, 1, 11, 5, 5, 5, 8, 14, 11, 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, 3, 7, 5, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 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, 193, 193, 73, 193, 73, 73, 73, 63, 42, 63, 63, 15, 7, 1, 1, 1, 1, 1, 1, 1, 73, 73, 201, 201, 201, 201, 201, 73, 73, 73, 73, 73, 42, 15, 15, 7, 7, 73, 73, 73, 73] 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: 654 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567559 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567559 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567559/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567559 Building REAL300025567560 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567560' /scratch/stefan/7901150/working/building/REAL300025567560 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025567560 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567560/0 /scratch/stefan/7901150/working/building/REAL300025567560 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 55) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/55 `/scratch/stefan/7901150/working/3D/55' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=NC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=C1Cl) `REAL300025567560.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567560.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567560/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567560 none CN1C=NC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 16, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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, 1, 11, 11, 11, 28, 82, 111, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 1, 28, 82, 82, 111, 111] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 17, 18, 22] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 23, 24, 25, 26, 27]) total number of confs: 645 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567560 none CN1C=NC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 16, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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, 137, 83, 137, 137, 21, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 83, 21, 21, 8, 8] 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]) total number of confs: 646 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567560 /scratch/stefan/7901150/working /scratch/stefan/7901150 mkdir: created directory `1' /scratch/stefan/7901150/working/building/REAL300025567560/1 /scratch/stefan/7901150/working/building/REAL300025567560 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 1 (index: 56) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/56 `/scratch/stefan/7901150/working/3D/56' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=NC(S(=O)(=O)[N-]CCC2=NC(=O)O[N-]2)=C1Cl) `REAL300025567560.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025567560.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567560/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567560 none CN1C=NC(S(=O)(=O)[N-]CCC2=NC(=O)O[N-]2)=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', '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, 1, 8, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 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: [1, 1, 1, 1, 1, 1, 13, 13, 13, 39, 105, 107, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 1, 105, 105, 107, 107] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 17, 18, 22] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 23, 24, 25, 26]) total number of confs: 536 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567560 none CN1C=NC(S(=O)(=O)[N-]CCC2=NC(=O)O[N-]2)=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', '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, 1, 8, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 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: [201, 201, 201, 201, 110, 40, 110, 110, 10, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 10, 10, 8, 8] 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]) total number of confs: 534 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567560 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567560 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 1: /scratch/stefan/7901150/working/building/REAL300025567560/1.* 0: /scratch/stefan/7901150/working/building/REAL300025567560/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567560 Building REAL300025567561 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567561' /scratch/stefan/7901150/working/building/REAL300025567561 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567561 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567561/0 /scratch/stefan/7901150/working/building/REAL300025567561 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 57) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/57 `/scratch/stefan/7901150/working/3D/57' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CCOC)S(=O)(=O)NCCC1=NC(=O)O[N-]1) `REAL300025567561.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567561.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567561/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567561 none COCCN(CCOC)S(=O)(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', '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, 12, 5, 5, 8, 5, 5, 12, 5, 14, 11, 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, 3, 7, 7, 7, 7, 7, 3, 7, 7, 6, 6, 4, 7, 7, 7, 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 79 conformations in input total number of sets (complete confs): 79 using faster count positions algorithm for large data unique positions, atoms: [72, 71, 59, 50, 43, 50, 73, 73, 74, 34, 43, 43, 15, 7, 1, 1, 1, 1, 1, 1, 1, 72, 72, 72, 71, 71, 59, 59, 73, 73, 73, 73, 74, 74, 74, 34, 15, 15, 7, 7] 79 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: 458 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567561 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567561 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567561/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567561 Building REAL300025567562 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567562' /scratch/stefan/7901150/working/building/REAL300025567562 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567562 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567562/0 /scratch/stefan/7901150/working/building/REAL300025567562 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 58) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/58 `/scratch/stefan/7901150/working/3D/58' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C(Br)=C1) `REAL300025567562.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567562.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567562/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567562 none CC1=CC=C(S(=O)(=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', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 17, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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 129 conformations in input total number of sets (complete confs): 129 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 33, 55, 129, 129, 129, 129, 129, 1, 1, 1, 2, 2, 2, 1, 1, 7, 33, 33, 55, 55, 1] 129 rigid atoms, others: [0, 1, 2, 3, 4, 5, 17, 18, 19, 23, 24, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 25, 26, 27, 28, 29]) total number of confs: 358 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567562 none CC1=CC=C(S(=O)(=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', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 17, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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 129 conformations in input total number of sets (complete confs): 129 using faster count positions algorithm for large data unique positions, atoms: [129, 129, 129, 129, 126, 96, 126, 126, 22, 8, 1, 1, 1, 1, 1, 1, 1, 129, 129, 129, 129, 129, 129, 129, 129, 96, 22, 22, 8, 8, 129] 129 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]) total number of confs: 463 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567562 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567562 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567562/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567562 Building REAL300025567563 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567563' /scratch/stefan/7901150/working/building/REAL300025567563 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567563 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567563/0 /scratch/stefan/7901150/working/building/REAL300025567563 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 59) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/59 `/scratch/stefan/7901150/working/3D/59' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2=CC=C(S(=O)(=O)NC3CC3)C=C2)[N-]O1) `REAL300025567563.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567563.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567563/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567563 none O=C1N=C(CCNS(=O)(=O)C2=CC=C(S(=O)(=O)NC3CC3)C=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.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: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 1, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 6, 6, 4, 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, 9, 20, 64, 88, 88, 88, 88, 88, 88, 88, 92, 92, 92, 156, 201, 201, 88, 88, 1, 1, 9, 9, 20, 20, 64, 88, 88, 156, 201, 201, 201, 201, 201, 88, 88] 201 rigid atoms, others: [0, 1, 2, 3, 4, 23, 24] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 789 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567563 none O=C1N=C(CCNS(=O)(=O)C2=CC=C(S(=O)(=O)NC3CC3)C=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.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: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 1, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 6, 6, 4, 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: [88, 88, 88, 31, 21, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 2, 2, 2, 7, 18, 18, 1, 1, 88, 88, 31, 31, 21, 21, 5, 1, 1, 7, 18, 18, 18, 18, 18, 1, 1] 201 rigid atoms, others: [38, 7, 10, 11, 12, 13, 14, 21, 22, 39, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37]) total number of confs: 268 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567563 none O=C1N=C(CCNS(=O)(=O)C2=CC=C(S(=O)(=O)NC3CC3)C=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.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: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 1, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 6, 6, 4, 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: [201, 201, 201, 105, 84, 38, 18, 18, 18, 18, 18, 18, 18, 16, 6, 16, 16, 1, 1, 1, 1, 18, 18, 201, 201, 105, 105, 84, 84, 38, 18, 18, 6, 1, 1, 1, 1, 1, 18, 18] 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, 39]) total number of confs: 604 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567563 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567563 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567563/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567563 Building REAL300025567564 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567564' /scratch/stefan/7901150/working/building/REAL300025567564 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567564 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567564/0 /scratch/stefan/7901150/working/building/REAL300025567564 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 60) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/60 `/scratch/stefan/7901150/working/3D/60' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1C(N)=O) `REAL300025567564.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567564.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567564/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567564 none CN1C=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 8, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in 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, 9, 49, 93, 201, 201, 201, 201, 201, 1, 1, 1, 4, 4, 2, 2, 2, 1, 9, 49, 49, 93, 93, 1, 4, 4] 201 rigid atoms, others: [0, 1, 2, 3, 4, 16, 17, 18, 24, 30] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 31, 32]) total number of confs: 600 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567564 none CN1C=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 8, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 139, 89, 139, 139, 24, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 89, 25, 25, 8, 8, 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]) total number of confs: 680 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567564 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567564 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567564/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567564 Building REAL300025567565 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567565' /scratch/stefan/7901150/working/building/REAL300025567565 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567565 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567565/0 /scratch/stefan/7901150/working/building/REAL300025567565 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 61) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/61 `/scratch/stefan/7901150/working/3D/61' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C1CCCCC1)S(=O)(=O)NCCC1=NC(=O)O[N-]1) `REAL300025567565.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567565/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567565 none CN(C1CCCCC1)S(=O)(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', '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, 8, 5, 5, 5, 5, 5, 5, 14, 11, 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, 6, 6, 4, 7, 7, 7, 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, 3, 12, 12, 12, 32, 90, 105, 201, 201, 201, 201, 201, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 90, 90, 105, 105] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 33, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 34, 35, 36, 37, 38, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22]) total number of confs: 625 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567565 none CN(C1CCCCC1)S(=O)(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', '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, 8, 5, 5, 5, 5, 5, 5, 14, 11, 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, 6, 6, 4, 7, 7, 7, 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: [161, 90, 161, 201, 201, 201, 201, 201, 51, 90, 90, 16, 8, 1, 1, 1, 1, 1, 1, 1, 161, 161, 161, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 51, 16, 16, 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]) total number of confs: 755 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567565 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567565 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567565/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567565 Building REAL300025567566 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567566' /scratch/stefan/7901150/working/building/REAL300025567566 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567566 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567566/0 /scratch/stefan/7901150/working/building/REAL300025567566 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 62) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/62 `/scratch/stefan/7901150/working/3D/62' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C(Cl)C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=C1) `REAL300025567566.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567566/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567566 none COC(=O)C1=CC=C(Cl)C(S(=O)(=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', 'C.ar', 'Cl', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 1, 16, 1, 14, 11, 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, 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: [11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 25, 43, 130, 130, 130, 130, 130, 1, 11, 11, 11, 1, 1, 5, 25, 25, 43, 43, 1] 201 rigid atoms, others: [33, 2, 4, 5, 6, 7, 8, 9, 10, 22, 26, 27] set([0, 1, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 28, 29, 30, 31, 32]) total number of confs: 339 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567566 none COC(=O)C1=CC=C(Cl)C(S(=O)(=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', 'C.ar', 'Cl', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 1, 16, 1, 14, 11, 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, 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, 130, 86, 130, 130, 24, 8, 1, 1, 1, 1, 1, 1, 1, 130, 201, 201, 201, 130, 130, 86, 24, 24, 8, 8, 130] 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: 787 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567566 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567566 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567566/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567566 Building REAL300025567567 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567567' /scratch/stefan/7901150/working/building/REAL300025567567 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567567 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567567/0 /scratch/stefan/7901150/working/building/REAL300025567567 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 63) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/63 `/scratch/stefan/7901150/working/3D/63' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C1CCCN1S(=O)(=O)NCCC1=NC(=O)O[N-]1) `REAL300025567567.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567567.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567567/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567567 none CCOC(=O)C1CCCN1S(=O)(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', '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, 12, 1, 11, 5, 5, 5, 5, 8, 14, 11, 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, 3, 7, 5, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 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, 9, 8, 1, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 14, 41, 41, 121, 121, 121, 121, 121, 20, 20, 20, 20, 20, 1, 1, 1, 1, 1, 1, 1, 14, 41, 41, 41, 41] 201 rigid atoms, others: [32, 33, 3, 5, 6, 7, 8, 9, 10, 27, 28, 29, 30, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 34, 35, 36, 37, 38]) total number of confs: 327 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567567 none CCOC(=O)C1CCCN1S(=O)(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', '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, 12, 1, 11, 5, 5, 5, 5, 8, 14, 11, 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, 3, 7, 5, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 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, 185, 185, 121, 185, 121, 121, 121, 121, 73, 41, 73, 73, 8, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 121, 121, 121, 121, 121, 121, 121, 41, 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]) total number of confs: 685 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567567 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567567 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567567/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567567 Building REAL300025567568 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567568' /scratch/stefan/7901150/working/building/REAL300025567568 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567568 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567568/0 /scratch/stefan/7901150/working/building/REAL300025567568 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 64) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/64 `/scratch/stefan/7901150/working/3D/64' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1) `REAL300025567568.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567568.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567568/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567568 none COCCOC1=CC=C(S(=O)(=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.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 5, 5, 12, 1, 1, 1, 1, 14, 11, 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, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 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: [24, 12, 7, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 19, 28, 79, 79, 79, 79, 79, 1, 1, 24, 24, 24, 12, 12, 7, 7, 1, 1, 7, 19, 19, 28, 28, 1, 1] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 21, 22, 38, 37, 30, 31] set([0, 1, 2, 3, 10, 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: 262 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567568 none COCCOC1=CC=C(S(=O)(=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.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 5, 5, 12, 1, 1, 1, 1, 14, 11, 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, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 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, 147, 129, 79, 58, 79, 79, 58, 46, 58, 58, 15, 8, 1, 1, 1, 1, 1, 1, 1, 79, 79, 201, 201, 201, 201, 201, 147, 147, 79, 79, 46, 16, 16, 8, 8, 79, 79] 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: 859 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567568 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567568 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567568/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567568 Building REAL300025567569 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567569' /scratch/stefan/7901150/working/building/REAL300025567569 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567569 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567569/0 /scratch/stefan/7901150/working/building/REAL300025567569 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 65) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/65 `/scratch/stefan/7901150/working/3D/65' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)C1=CC=C(Cl)C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=C1) `REAL300025567569.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567569.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567569/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567569 none CS(=O)(=O)C1=CC=C(Cl)C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 14, 11, 11, 1, 1, 1, 1, 16, 1, 14, 11, 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, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 6, 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 179 conformations in input total number of sets (complete confs): 179 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 15, 45, 64, 143, 143, 143, 143, 143, 1, 3, 3, 3, 1, 1, 15, 45, 45, 64, 64, 1] 179 rigid atoms, others: [1, 33, 4, 5, 6, 7, 8, 9, 10, 22, 26, 27] set([0, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 28, 29, 30, 31, 32]) total number of confs: 413 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567569 none CS(=O)(=O)C1=CC=C(Cl)C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 14, 11, 11, 1, 1, 1, 1, 16, 1, 14, 11, 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, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 6, 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 179 conformations in input total number of sets (complete confs): 179 using faster count positions algorithm for large data unique positions, atoms: [179, 143, 179, 179, 143, 142, 143, 143, 143, 129, 93, 129, 129, 24, 8, 1, 1, 1, 1, 1, 1, 1, 143, 179, 179, 179, 142, 143, 93, 24, 24, 8, 8, 143] 179 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: 724 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567569 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567569 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567569/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567569 Building REAL300025567570 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567570' /scratch/stefan/7901150/working/building/REAL300025567570 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567570 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567570/0 /scratch/stefan/7901150/working/building/REAL300025567570 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 66) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/66 `/scratch/stefan/7901150/working/3D/66' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1Cl) `REAL300025567570.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567570.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567570/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567570 none COC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 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, 2, 2, 2, 9, 37, 55, 133, 133, 133, 133, 133, 1, 1, 1, 3, 3, 3, 1, 1, 9, 37, 37, 55, 55, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 18, 19, 20, 24, 25, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 26, 27, 28, 29, 30]) total number of confs: 370 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567570 none COC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 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, 133, 133, 133, 133, 87, 59, 87, 87, 20, 8, 1, 1, 1, 1, 1, 1, 1, 133, 133, 133, 201, 201, 201, 133, 133, 59, 20, 20, 8, 8, 133] 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]) total number of confs: 578 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567570 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567570 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567570/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567570 Building REAL300025567571 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567571' /scratch/stefan/7901150/working/building/REAL300025567571 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567571 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567571/0 /scratch/stefan/7901150/working/building/REAL300025567571 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 67) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/67 `/scratch/stefan/7901150/working/3D/67' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1F) `REAL300025567571.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567571/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567571 none COC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 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, 2, 2, 2, 9, 41, 61, 135, 135, 135, 135, 135, 1, 1, 1, 3, 3, 3, 1, 1, 9, 41, 41, 61, 61, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 18, 19, 20, 24, 25, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 26, 27, 28, 29, 30]) total number of confs: 389 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567571 none COC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 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, 135, 135, 135, 135, 83, 57, 83, 83, 20, 8, 1, 1, 1, 1, 1, 1, 1, 135, 135, 135, 201, 201, 201, 135, 135, 57, 21, 21, 8, 8, 135] 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]) total number of confs: 572 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567571 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567571 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567571/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567571 Building REAL300025567572 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567572' /scratch/stefan/7901150/working/building/REAL300025567572 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567572 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567572/0 /scratch/stefan/7901150/working/building/REAL300025567572 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 68) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/68 `/scratch/stefan/7901150/working/3D/68' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1C) `REAL300025567572.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567572.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567572/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567572 none COC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 5, 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, 6, 4, 7, 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, 3, 3, 3, 9, 39, 68, 174, 174, 174, 174, 174, 1, 1, 1, 4, 4, 4, 1, 1, 9, 39, 39, 68, 68, 1, 2, 2, 2] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 18, 19, 20, 24, 25, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 26, 27, 28, 29, 30, 32, 33, 34]) total number of confs: 488 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567572 none COC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 5, 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, 6, 4, 7, 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, 174, 174, 174, 174, 115, 68, 115, 115, 20, 8, 1, 1, 1, 1, 1, 1, 1, 174, 174, 174, 201, 201, 201, 174, 174, 68, 20, 20, 8, 8, 174, 174, 174, 174] 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: 631 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567572 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567572 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567572/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567572 Building REAL300025567573 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567573' /scratch/stefan/7901150/working/building/REAL300025567573 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567573 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567573/0 /scratch/stefan/7901150/working/building/REAL300025567573 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 69) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/69 `/scratch/stefan/7901150/working/3D/69' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1C) `REAL300025567573.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567573/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567573 none CCOC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 5, 12, 1, 1, 1, 1, 14, 11, 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, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 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: [15, 7, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 35, 55, 140, 140, 140, 140, 140, 1, 1, 1, 15, 15, 15, 15, 15, 1, 1, 9, 35, 35, 55, 55, 1, 2, 2, 2] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 34, 19, 20, 21, 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, 35, 36, 37]) total number of confs: 417 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567573 none CCOC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 5, 12, 1, 1, 1, 1, 14, 11, 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, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 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, 199, 84, 84, 140, 140, 84, 59, 84, 84, 18, 8, 1, 1, 1, 1, 1, 1, 1, 140, 140, 140, 201, 201, 201, 201, 201, 140, 140, 59, 18, 18, 8, 8, 140, 140, 140, 140] 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: 789 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567573 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567573 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567573/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567573 Building REAL300025567574 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567574' /scratch/stefan/7901150/working/building/REAL300025567574 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567574 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567574/0 /scratch/stefan/7901150/working/building/REAL300025567574 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 70) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/70 `/scratch/stefan/7901150/working/3D/70' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1C(N)=O) `REAL300025567574.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567574.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567574/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567574 none CC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1C(N)=O 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.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', '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, 1, 8, 1, 11, 12, 8, 1, 1, 1, 8, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 4, 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: [1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 49, 72, 177, 177, 177, 177, 177, 1, 1, 1, 4, 4, 2, 2, 2, 1, 1, 9, 49, 49, 72, 72, 1, 4, 4] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 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, 33, 34]) total number of confs: 470 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567574 none CC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1C(N)=O 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.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', '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, 1, 8, 1, 11, 12, 8, 1, 1, 1, 8, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 4, 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: [177, 177, 177, 177, 120, 83, 120, 120, 24, 8, 1, 1, 1, 1, 1, 1, 1, 177, 177, 177, 201, 201, 177, 177, 177, 177, 177, 83, 24, 24, 8, 8, 177, 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: 688 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567574 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567574 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567574/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567574 Building REAL300025567575 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567575' /scratch/stefan/7901150/working/building/REAL300025567575 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567575 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567575/0 /scratch/stefan/7901150/working/building/REAL300025567575 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 71) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/71 `/scratch/stefan/7901150/working/3D/71' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1C(N)=O) `REAL300025567575.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567575.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567575/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567575 none COC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 8, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 4, 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: [3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 43, 61, 138, 138, 138, 138, 138, 1, 1, 1, 4, 4, 4, 4, 4, 1, 1, 9, 43, 43, 61, 61, 1, 4, 4] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 33, 18, 19, 20, 26, 27] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 34, 35]) total number of confs: 397 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567575 none COC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 8, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 4, 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: [201, 138, 138, 138, 138, 96, 63, 96, 96, 22, 8, 1, 1, 1, 1, 1, 1, 1, 138, 138, 138, 201, 201, 201, 201, 201, 138, 138, 63, 22, 22, 8, 8, 138, 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]) total number of confs: 812 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567575 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567575 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567575/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567575 Building REAL300025567576 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567576' /scratch/stefan/7901150/working/building/REAL300025567576 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567576 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567576/0 /scratch/stefan/7901150/working/building/REAL300025567576 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 72) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/72 `/scratch/stefan/7901150/working/3D/72' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)OC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C2=CC=CC=C12) `REAL300025567576.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567576/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567576 none CC(C)OC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C2=CC=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 1, 1, 1, 1, 14, 11, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 3, 5, 25, 44, 135, 135, 135, 135, 135, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 1, 1, 5, 25, 25, 44, 44, 1, 1, 1, 1] 201 rigid atoms, others: [33, 34, 3, 4, 5, 6, 7, 8, 41, 42, 43, 40, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39]) total number of confs: 358 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567576 none CC(C)OC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C2=CC=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 1, 1, 1, 1, 14, 11, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 135, 135, 135, 135, 135, 83, 135, 135, 24, 8, 1, 1, 1, 1, 1, 1, 1, 135, 135, 135, 135, 135, 135, 201, 201, 201, 201, 201, 201, 201, 135, 135, 83, 24, 24, 8, 8, 135, 135, 135, 135] 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: 651 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567576 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567576 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567576/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567576 Building REAL300025567577 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567577' /scratch/stefan/7901150/working/building/REAL300025567577 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567577 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567577/0 /scratch/stefan/7901150/working/building/REAL300025567577 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 73) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/73 `/scratch/stefan/7901150/working/3D/73' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(C1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1)N1CCOCC1) `REAL300025567577.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567577.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567577/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567577 none O=C(C1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1)N1CCOCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'N.am', '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'] dock atom type numbers: [11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 5, 5, 12, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 31, 46, 130, 130, 130, 130, 130, 1, 1, 6, 13, 13, 13, 13, 13, 1, 1, 9, 31, 31, 46, 46, 1, 1, 13, 13, 13, 13, 13, 13, 13, 13] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 33, 34, 18, 19, 26, 27] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 343 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567577 none O=C(C1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1)N1CCOCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'N.am', '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'] dock atom type numbers: [11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 5, 5, 12, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 130, 130, 130, 130, 95, 63, 95, 95, 20, 8, 1, 1, 1, 1, 1, 1, 1, 130, 130, 147, 201, 201, 201, 201, 201, 130, 130, 63, 20, 20, 8, 8, 130, 130, 201, 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, 41, 42]) 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567577 none O=C(C1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1)N1CCOCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'N.am', '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'] dock atom type numbers: [11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 5, 5, 12, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 13, 13, 9, 12, 17, 17, 17, 37, 83, 115, 201, 201, 201, 201, 201, 13, 13, 1, 1, 1, 1, 1, 1, 13, 13, 37, 83, 83, 115, 115, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 35, 36, 37, 38, 39, 40, 41, 42, 20, 21, 22, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 691 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567577 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567577 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567577/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567577 Building REAL300025567578 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567578' /scratch/stefan/7901150/working/building/REAL300025567578 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567578 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567578/0 /scratch/stefan/7901150/working/building/REAL300025567578 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 74) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/74 `/scratch/stefan/7901150/working/3D/74' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC([N+](=O)[O-])=CC=C1S(=O)(=O)NCCC1=NC(=O)O[N-]1) `REAL300025567578.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567578.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567578/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567578 none CC1=CC([N+](=O)[O-])=CC=C1S(=O)(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.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, 8, 11, 11, 1, 1, 1, 14, 11, 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, 3, 3, 7, 7, 7, 7, 6, 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 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, 2, 2, 1, 1, 1, 1, 5, 5, 5, 13, 38, 62, 146, 146, 146, 146, 146, 2, 2, 2, 1, 1, 1, 13, 40, 40, 62, 62] 146 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 25, 26, 27] set([32, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31]) total number of confs: 417 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567578 none CC1=CC([N+](=O)[O-])=CC=C1S(=O)(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.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, 8, 11, 11, 1, 1, 1, 14, 11, 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, 3, 3, 7, 7, 7, 7, 6, 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 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, 136, 136, 146, 146, 146, 146, 136, 86, 136, 136, 24, 8, 1, 1, 1, 1, 1, 1, 1, 146, 146, 146, 146, 146, 146, 86, 24, 24, 8, 8] 146 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: 615 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567578 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567578 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567578/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567578 Building REAL300025567579 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567579' /scratch/stefan/7901150/working/building/REAL300025567579 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567579 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567579/0 /scratch/stefan/7901150/working/building/REAL300025567579 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 75) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/75 `/scratch/stefan/7901150/working/3D/75' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2=C(Cl)C=C3CCC(=O)NC3=C2)[N-]O1) `REAL300025567579.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567579.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567579/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567579 none O=C1N=C(CCNS(=O)(=O)C2=C(Cl)C=C3CCC(=O)NC3=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 16, 1, 1, 5, 5, 1, 11, 8, 1, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 3, 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, 9, 25, 96, 155, 155, 155, 166, 166, 166, 166, 166, 166, 166, 166, 166, 166, 166, 1, 1, 9, 9, 25, 25, 96, 166, 166, 166, 166, 166, 166, 166] 166 rigid atoms, others: [0, 1, 2, 3, 4, 22, 23] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 603 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567579 none O=C1N=C(CCNS(=O)(=O)C2=C(Cl)C=C3CCC(=O)NC3=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 16, 1, 1, 5, 5, 1, 11, 8, 1, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 3, 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, 84, 56, 13, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 166, 166, 84, 84, 56, 56, 13, 1, 1, 1, 1, 1, 1, 1] 166 rigid atoms, others: [32, 33, 34, 35, 7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 501 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567579 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567579 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567579/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567579 Building REAL300025567580 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567580' /scratch/stefan/7901150/working/building/REAL300025567580 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567580 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567580/0 /scratch/stefan/7901150/working/building/REAL300025567580 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 76) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/76 `/scratch/stefan/7901150/working/3D/76' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)C1=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=CN1C) `REAL300025567580.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567580.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567580/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567580 none CNC(=O)C1=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=CN1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 5, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 6, 6, 4, 7, 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, 1, 6, 1, 1, 1, 1, 2, 2, 2, 9, 51, 87, 201, 201, 201, 201, 201, 1, 1, 1, 6, 6, 6, 6, 1, 9, 51, 51, 87, 87, 1, 2, 2, 2] 201 rigid atoms, others: [32, 2, 4, 5, 6, 7, 19, 20, 21, 26] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 27, 28, 29, 30, 31, 33, 34, 35]) total number of confs: 579 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567580 none CNC(=O)C1=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=CN1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 5, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 6, 6, 4, 7, 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, 133, 80, 133, 133, 24, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 80, 25, 25, 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]) total number of confs: 653 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567580 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567580 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567580/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567580 Building REAL300025567581 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567581' /scratch/stefan/7901150/working/building/REAL300025567581 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567581 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567581/0 /scratch/stefan/7901150/working/building/REAL300025567581 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 77) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/77 `/scratch/stefan/7901150/working/3D/77' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(Cl)C=C1S(=O)(=O)NCCC1=NC(=O)O[N-]1) `REAL300025567581.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567581.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567581/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567581 none CC1=CC=C(Cl)C=C1S(=O)(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.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, 1, 16, 1, 1, 14, 11, 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, 6, 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 175 conformations in input total number of sets (complete confs): 175 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 13, 53, 83, 175, 175, 175, 175, 175, 2, 2, 2, 1, 1, 1, 13, 55, 55, 83, 83] 175 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 23, 24, 25] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30]) total number of confs: 500 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567581 none CC1=CC=C(Cl)C=C1S(=O)(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.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, 1, 16, 1, 1, 14, 11, 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, 6, 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 175 conformations in input total number of sets (complete confs): 175 using faster count positions algorithm for large data unique positions, atoms: [175, 175, 175, 175, 175, 175, 175, 165, 99, 165, 165, 24, 8, 1, 1, 1, 1, 1, 1, 1, 175, 175, 175, 175, 175, 175, 99, 24, 24, 8, 8] 175 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: 654 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567581 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567581 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567581/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567581 Building REAL300025567582 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567582' /scratch/stefan/7901150/working/building/REAL300025567582 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567582 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567582/0 /scratch/stefan/7901150/working/building/REAL300025567582 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 78) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/78 `/scratch/stefan/7901150/working/3D/78' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)COC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1) `REAL300025567582.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567582.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567582/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567582 none CC(C)COC1=CC=C(S(=O)(=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.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 12, 1, 1, 1, 1, 14, 11, 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, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 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, 5, 9, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 27, 44, 126, 126, 126, 126, 126, 1, 1, 9, 9, 9, 9, 9, 9, 9, 5, 5, 1, 1, 9, 27, 27, 44, 44, 1, 1] 201 rigid atoms, others: [32, 33, 4, 5, 6, 7, 8, 9, 39, 40, 21, 22] set([0, 1, 2, 3, 10, 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: 359 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567582 none CC(C)COC1=CC=C(S(=O)(=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.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 12, 1, 1, 1, 1, 14, 11, 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, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 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, 194, 126, 75, 126, 126, 75, 58, 75, 75, 16, 8, 1, 1, 1, 1, 1, 1, 1, 126, 126, 201, 201, 201, 201, 201, 201, 201, 201, 201, 126, 126, 58, 17, 17, 8, 8, 126, 126] 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: 815 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567582 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567582 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567582/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567582 Building REAL300025567583 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567583' /scratch/stefan/7901150/working/building/REAL300025567583 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567583 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567583/0 /scratch/stefan/7901150/working/building/REAL300025567583 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 79) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/79 `/scratch/stefan/7901150/working/3D/79' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2=CC=C3NC(=O)CCCC3=C2)[N-]O1) `REAL300025567583.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567583.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567583/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567583 none O=C1N=C(CCNS(=O)(=O)C2=CC=C3NC(=O)CCCC3=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', '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: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in 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, 25, 83, 114, 114, 114, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 9, 9, 25, 25, 83, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 22, 23] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 604 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567583 none O=C1N=C(CCNS(=O)(=O)C2=CC=C3NC(=O)CCCC3=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', '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: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 94, 57, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 94, 94, 57, 57, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 571 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567583 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567583 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567583/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567583 Building REAL300025567584 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567584' /scratch/stefan/7901150/working/building/REAL300025567584 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567584 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567584/0 /scratch/stefan/7901150/working/building/REAL300025567584 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 80) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/80 `/scratch/stefan/7901150/working/3D/80' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=C(C)C=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1C) `REAL300025567584.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567584.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567584/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567584 none COC1=C(C)C=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 12, 1, 1, 5, 1, 1, 14, 11, 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, 3, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 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, 2, 2, 2, 9, 33, 55, 151, 151, 151, 151, 151, 1, 1, 1, 3, 3, 3, 2, 2, 2, 1, 9, 33, 33, 55, 55, 1, 2, 2, 2] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 34, 19, 20, 21, 28] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 35, 36, 37]) total number of confs: 385 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567584 none COC1=C(C)C=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 12, 1, 1, 5, 1, 1, 14, 11, 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, 3, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 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, 145, 145, 151, 151, 151, 145, 93, 145, 145, 24, 8, 1, 1, 1, 1, 1, 1, 1, 151, 151, 151, 201, 201, 201, 151, 151, 151, 151, 93, 24, 24, 8, 8, 151, 151, 151, 151] 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: 697 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567584 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567584 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567584/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567584 Building REAL300025567585 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567585' /scratch/stefan/7901150/working/building/REAL300025567585 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567585 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567585/0 /scratch/stefan/7901150/working/building/REAL300025567585 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 81) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/81 `/scratch/stefan/7901150/working/3D/81' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1Cl) `REAL300025567585.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567585.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567585/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567585 none N#CC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1Cl NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 16, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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, 1, 1, 2, 2, 2, 9, 49, 88, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 9, 49, 49, 88, 88, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 18, 19, 20, 21, 22, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27]) total number of confs: 554 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567585 none N#CC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1Cl NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 16, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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, 116, 88, 116, 116, 24, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 88, 25, 25, 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]) total number of confs: 607 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567585 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567585 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567585/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567585 Building REAL300025567586 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567586' /scratch/stefan/7901150/working/building/REAL300025567586 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567586 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567586/0 /scratch/stefan/7901150/working/building/REAL300025567586 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 82) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/82 `/scratch/stefan/7901150/working/3D/82' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=CC=C1Cl) `REAL300025567586.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567586.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567586/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567586 none N#CC1=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=CC=C1Cl NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 16, 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, 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, 2, 2, 2, 9, 51, 88, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 9, 51, 51, 88, 88, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 17, 18, 19, 20, 21, 27, 28] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26]) total number of confs: 558 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567586 none N#CC1=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=CC=C1Cl NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 16, 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, 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, 134, 90, 134, 134, 24, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 90, 25, 25, 8, 8, 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]) total number of confs: 659 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567586 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567586 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567586/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567586 Building REAL300025567587 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567587' /scratch/stefan/7901150/working/building/REAL300025567587 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567587 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567587/0 /scratch/stefan/7901150/working/building/REAL300025567587 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 83) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/83 `/scratch/stefan/7901150/working/3D/83' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2=CC=C3COC(=O)C3=C2)[N-]O1) `REAL300025567587.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567587.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567587/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567587 none O=C1N=C(CCNS(=O)(=O)C2=CC=C3COC(=O)C3=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', '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, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 5, 12, 1, 11, 1, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 3, 7, 5, 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: [1, 1, 1, 1, 1, 9, 25, 91, 139, 139, 139, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 9, 9, 25, 25, 91, 201, 201, 201, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 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: 664 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567587 none O=C1N=C(CCNS(=O)(=O)C2=CC=C3COC(=O)C3=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', '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, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 5, 12, 1, 11, 1, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 3, 7, 5, 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: [201, 201, 201, 84, 52, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 84, 84, 52, 52, 9, 1, 1, 1, 1, 1] 201 rigid atoms, others: [7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 538 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567587 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567587 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567587/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567587 Building REAL300025567588 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567588' /scratch/stefan/7901150/working/building/REAL300025567588 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567588 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567588/0 /scratch/stefan/7901150/working/building/REAL300025567588 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 84) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/84 `/scratch/stefan/7901150/working/3D/84' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C2=CC=CN=C12) `REAL300025567588.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567588.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567588/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567588 none COC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C2=CC=CN=C12 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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.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, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 8, 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, 6, 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, 1, 3, 3, 3, 5, 29, 56, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 5, 29, 29, 56, 56, 1, 1, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 34, 18, 19, 20, 21, 22, 23, 36, 27, 28, 35] set([0, 32, 33, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 29, 30, 31]) total number of confs: 440 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567588 none COC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C2=CC=CN=C12 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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.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, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 8, 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, 6, 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, 201, 201, 201, 201, 201, 101, 201, 201, 24, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 101, 24, 24, 8, 8, 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]) total number of confs: 806 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567588 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567588 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567588/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567588 Building REAL300025567589 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567589' /scratch/stefan/7901150/working/building/REAL300025567589 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567589 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567589/0 /scratch/stefan/7901150/working/building/REAL300025567589 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 85) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/85 `/scratch/stefan/7901150/working/3D/85' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1Cl) `REAL300025567589.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567589.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567589/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567589 none CC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1Cl 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.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'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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, 2, 2, 2, 9, 51, 89, 201, 201, 201, 201, 201, 1, 1, 1, 2, 2, 2, 1, 1, 9, 51, 51, 89, 89, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 17, 18, 19, 23, 24, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 25, 26, 27, 28, 29]) total number of confs: 563 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567589 none CC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1Cl 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.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'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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, 121, 81, 121, 121, 24, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 81, 24, 24, 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]) total number of confs: 649 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567589 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567589 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567589/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567589 Building REAL300025567590 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567590' /scratch/stefan/7901150/working/building/REAL300025567590 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567590 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567590/0 /scratch/stefan/7901150/working/building/REAL300025567590 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 86) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/86 `/scratch/stefan/7901150/working/3D/86' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2=CC=CC(Cl)=C2F)[N-]O1) `REAL300025567590.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567590.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567590/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567590 none O=C1N=C(CCNS(=O)(=O)C2=CC=CC(Cl)=C2F)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 16, 1, 15, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 9, 21, 78, 131, 131, 131, 201, 201, 201, 201, 201, 201, 201, 1, 1, 9, 9, 21, 21, 78, 201, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 18, 19] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 616 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567590 none O=C1N=C(CCNS(=O)(=O)C2=CC=CC(Cl)=C2F)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 16, 1, 15, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 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: [201, 201, 201, 100, 72, 25, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 100, 100, 72, 72, 25, 1, 1, 1] 201 rigid atoms, others: [7, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 611 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567590 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567590 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567590/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567590 Building REAL300025567591 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567591' /scratch/stefan/7901150/working/building/REAL300025567591 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567591 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567591/0 /scratch/stefan/7901150/working/building/REAL300025567591 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 87) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/87 `/scratch/stefan/7901150/working/3D/87' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=CC=C1OC(C)C) `REAL300025567591.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567591.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567591/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567591 none CC1=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=CC=C1OC(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 1, 1, 14, 11, 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, 7, 7, 7, 6, 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: [1, 1, 1, 1, 1, 2, 2, 2, 9, 32, 50, 142, 142, 142, 142, 142, 1, 1, 1, 1, 5, 9, 9, 2, 2, 2, 1, 9, 32, 32, 50, 50, 1, 1, 9, 9, 9, 9, 9, 9, 9] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 16, 17, 18, 19, 26] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 387 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567591 none CC1=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=CC=C1OC(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 1, 1, 14, 11, 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, 7, 7, 7, 6, 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: [142, 142, 142, 81, 58, 81, 81, 18, 8, 1, 1, 1, 1, 1, 1, 1, 142, 142, 142, 142, 201, 201, 201, 142, 142, 142, 142, 58, 18, 18, 8, 8, 142, 142, 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]) total number of confs: 553 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567591 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567591 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567591/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567591 Building REAL300025567592 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567592' /scratch/stefan/7901150/working/building/REAL300025567592 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567592 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567592/0 /scratch/stefan/7901150/working/building/REAL300025567592 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 88) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/88 `/scratch/stefan/7901150/working/3D/88' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC([N+](=O)[O-])=CC=C1S(=O)(=O)NCCC1=NC(=O)O[N-]1) `REAL300025567592.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567592.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567592/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567592 none COC1=CC([N+](=O)[O-])=CC=C1S(=O)(=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', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.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, 14, 11, 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, 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, 1, 1, 7, 7, 7, 21, 72, 98, 201, 201, 201, 201, 201, 4, 4, 4, 1, 1, 1, 21, 72, 72, 98, 98] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 26, 27, 28] set([0, 32, 33, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31]) total number of confs: 605 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567592 none COC1=CC([N+](=O)[O-])=CC=C1S(=O)(=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', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.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, 14, 11, 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, 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, 187, 201, 201, 201, 201, 201, 145, 92, 145, 145, 24, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 92, 24, 24, 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: 726 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567592 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567592 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567592/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567592 Building REAL300025567593 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567593' /scratch/stefan/7901150/working/building/REAL300025567593 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567593 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567593/0 /scratch/stefan/7901150/working/building/REAL300025567593 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 89) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/89 `/scratch/stefan/7901150/working/3D/89' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C2=CC=CC=C12) `REAL300025567593.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567593.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567593/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567593 none COC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C2=CC=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 12, 1, 1, 1, 1, 14, 11, 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, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 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, 3, 5, 29, 62, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 5, 29, 29, 62, 62, 1, 1, 1, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 34, 18, 19, 20, 21, 22, 23, 36, 27, 28, 37, 35] set([0, 32, 33, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 29, 30, 31]) total number of confs: 473 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567593 none COC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C2=CC=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 12, 1, 1, 1, 1, 14, 11, 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, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 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, 102, 201, 201, 24, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 102, 25, 24, 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]) total number of confs: 791 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567593 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567593 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567593/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567593 Building REAL300025567594 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567594' /scratch/stefan/7901150/working/building/REAL300025567594 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567594 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567594/0 /scratch/stefan/7901150/working/building/REAL300025567594 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 90) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/90 `/scratch/stefan/7901150/working/3D/90' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1F) `REAL300025567594.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567594.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567594/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567594 none CC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1F 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.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'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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, 2, 2, 2, 9, 53, 91, 201, 201, 201, 201, 201, 1, 1, 1, 2, 2, 2, 1, 1, 9, 53, 53, 91, 91, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 17, 18, 19, 23, 24, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 25, 26, 27, 28, 29]) total number of confs: 565 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567594 none CC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1F 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.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'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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, 123, 81, 123, 123, 24, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 81, 24, 24, 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]) total number of confs: 657 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567594 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567594 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567594/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567594 Building REAL300025567595 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567595' /scratch/stefan/7901150/working/building/REAL300025567595 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025567595 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567595/0 /scratch/stefan/7901150/working/building/REAL300025567595 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 91) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/91 `/scratch/stefan/7901150/working/3D/91' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2=C(Cl)C=C(Cl)C=C2Cl)[N-]O1) `REAL300025567595.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567595.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567595/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567595 none O=C1N=C(CCNS(=O)(=O)C2=C(Cl)C=C(Cl)C=C2Cl)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 16, 1, 1, 16, 1, 1, 16, 8, 12, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 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: [1, 1, 1, 1, 1, 9, 25, 111, 193, 193, 193, 201, 201, 201, 193, 201, 201, 201, 201, 1, 1, 9, 9, 25, 25, 111, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 19, 20] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 772 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567595 none O=C1N=C(CCNS(=O)(=O)C2=C(Cl)C=C(Cl)C=C2Cl)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 16, 1, 1, 16, 1, 1, 16, 8, 12, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 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: [201, 201, 201, 99, 64, 17, 9, 1, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 99, 99, 64, 64, 17, 1, 1] 201 rigid atoms, others: [7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 600 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567595 /scratch/stefan/7901150/working /scratch/stefan/7901150 mkdir: created directory `1' /scratch/stefan/7901150/working/building/REAL300025567595/1 /scratch/stefan/7901150/working/building/REAL300025567595 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 1 (index: 92) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/92 `/scratch/stefan/7901150/working/3D/92' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CC[N-]S(=O)(=O)C2=C(Cl)C=C(Cl)C=C2Cl)[N-]O1) `REAL300025567595.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025567595.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567595/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567595 none O=C1N=C(CC[N-]S(=O)(=O)C2=C(Cl)C=C(Cl)C=C2Cl)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 16, 1, 1, 16, 1, 1, 16, 8, 12, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 9, 13, 44, 96, 96, 96, 100, 100, 100, 98, 100, 100, 100, 100, 1, 1, 9, 9, 13, 13, 100, 100] 100 rigid atoms, others: [0, 1, 2, 3, 4, 19, 20] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26]) total number of confs: 357 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567595 none O=C1N=C(CC[N-]S(=O)(=O)C2=C(Cl)C=C(Cl)C=C2Cl)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 16, 1, 1, 16, 1, 1, 16, 8, 12, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 47, 43, 16, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 100, 100, 47, 47, 43, 43, 1, 1] 100 rigid atoms, others: [7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 19, 20, 21, 22, 23, 24]) total number of confs: 261 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567595 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567595 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 1: /scratch/stefan/7901150/working/building/REAL300025567595/1.* 0: /scratch/stefan/7901150/working/building/REAL300025567595/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567595 Building REAL300025567596 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567596' /scratch/stefan/7901150/working/building/REAL300025567596 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567596 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567596/0 /scratch/stefan/7901150/working/building/REAL300025567596 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 93) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/93 `/scratch/stefan/7901150/working/3D/93' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(Cl)=CC=C1S(=O)(=O)NCCC1=NC(=O)O[N-]1) `REAL300025567596.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567596.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567596/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567596 none CC1=CC(Cl)=CC=C1S(=O)(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.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, 16, 1, 1, 1, 14, 11, 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, 6, 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 154 conformations in input total number of sets (complete confs): 154 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 13, 40, 64, 154, 154, 154, 154, 154, 2, 2, 2, 1, 1, 1, 13, 42, 42, 64, 64] 154 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 23, 24, 25] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30]) total number of confs: 413 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567596 none CC1=CC(Cl)=CC=C1S(=O)(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.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, 16, 1, 1, 1, 14, 11, 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, 6, 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 154 conformations in input total number of sets (complete confs): 154 using faster count positions algorithm for large data unique positions, atoms: [154, 154, 154, 144, 154, 154, 154, 144, 89, 144, 144, 24, 8, 1, 1, 1, 1, 1, 1, 1, 154, 154, 154, 154, 154, 154, 89, 24, 24, 8, 8] 154 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: 629 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567596 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567596 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567596/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567596 Building REAL300025567597 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567597' /scratch/stefan/7901150/working/building/REAL300025567597 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567597 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567597/0 /scratch/stefan/7901150/working/building/REAL300025567597 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 94) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/94 `/scratch/stefan/7901150/working/3D/94' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(F)C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=C1) `REAL300025567597.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567597.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567597/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567597 none CC1=CC=C(F)C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 1, 1, 1, 1, 15, 1, 14, 11, 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, 7, 7, 7, 7, 7, 7, 7, 6, 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, 1, 7, 7, 7, 25, 77, 98, 201, 201, 201, 201, 201, 1, 2, 2, 2, 1, 1, 25, 77, 77, 98, 98, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 19, 23, 24, 30] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 25, 26, 27, 28, 29]) total number of confs: 605 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567597 none CC1=CC=C(F)C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 1, 1, 1, 1, 15, 1, 14, 11, 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, 7, 7, 7, 7, 7, 7, 7, 6, 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, 128, 68, 128, 128, 20, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 68, 20, 20, 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]) total number of confs: 646 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567597 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567597 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567597/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567597 Building REAL300025567598 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567598' /scratch/stefan/7901150/working/building/REAL300025567598 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567598 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567598/0 /scratch/stefan/7901150/working/building/REAL300025567598 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 95) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/95 `/scratch/stefan/7901150/working/3D/95' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(F)C=C1S(=O)(=O)NCCC1=NC(=O)O[N-]1) `REAL300025567598.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567598.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567598/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567598 none CC1=CC=C(F)C=C1S(=O)(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.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, 1, 15, 1, 1, 14, 11, 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, 6, 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 168 conformations in input total number of sets (complete confs): 168 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 13, 50, 79, 168, 168, 168, 168, 168, 2, 2, 2, 1, 1, 1, 13, 52, 52, 79, 79] 168 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 23, 24, 25] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30]) total number of confs: 476 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567598 none CC1=CC=C(F)C=C1S(=O)(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.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, 1, 15, 1, 1, 14, 11, 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, 6, 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 168 conformations in input total number of sets (complete confs): 168 using faster count positions algorithm for large data unique positions, atoms: [168, 168, 168, 168, 168, 168, 168, 157, 87, 157, 157, 24, 8, 1, 1, 1, 1, 1, 1, 1, 168, 168, 168, 168, 168, 168, 87, 24, 24, 8, 8] 168 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: 667 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567598 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567598 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567598/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567598 Building REAL300025567599 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567599' /scratch/stefan/7901150/working/building/REAL300025567599 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567599 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567599/0 /scratch/stefan/7901150/working/building/REAL300025567599 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 96) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/96 `/scratch/stefan/7901150/working/3D/96' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2=CC=C(F)C=C2Br)[N-]O1) `REAL300025567599.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567599.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567599/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567599 none O=C1N=C(CCNS(=O)(=O)C2=CC=C(F)C=C2Br)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 15, 1, 1, 17, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [1, 1, 1, 1, 1, 9, 22, 93, 125, 125, 125, 129, 129, 129, 129, 129, 129, 129, 1, 1, 9, 9, 22, 22, 93, 129, 129, 129] 129 rigid atoms, others: [0, 1, 2, 3, 4, 18, 19] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 466 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567599 none O=C1N=C(CCNS(=O)(=O)C2=CC=C(F)C=C2Br)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 15, 1, 1, 17, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [129, 129, 129, 56, 34, 7, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 129, 129, 56, 56, 34, 34, 7, 1, 1, 1] 129 rigid atoms, others: [7, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 355 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567599 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567599 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567599/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567599 Building REAL300025567600 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567600' /scratch/stefan/7901150/working/building/REAL300025567600 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567600 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567600/0 /scratch/stefan/7901150/working/building/REAL300025567600 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 97) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/97 `/scratch/stefan/7901150/working/3D/97' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2=CC=C(CCCl)C=C2)[N-]O1) `REAL300025567600.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567600.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567600/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567600 none O=C1N=C(CCNS(=O)(=O)C2=CC=C(CCCl)C=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'Cl', 'C.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 5, 5, 16, 1, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 9, 24, 72, 96, 96, 96, 96, 96, 96, 96, 156, 201, 96, 96, 1, 1, 9, 9, 24, 24, 72, 96, 96, 156, 156, 201, 201, 96, 96] 201 rigid atoms, others: [0, 1, 2, 3, 4, 19, 20] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 979 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567600 none O=C1N=C(CCNS(=O)(=O)C2=CC=C(CCCl)C=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'Cl', 'C.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 5, 5, 16, 1, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [96, 96, 96, 41, 25, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 1, 1, 96, 96, 41, 41, 25, 25, 5, 1, 1, 2, 2, 6, 6, 1, 1] 201 rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 12, 13, 14, 17, 18, 26, 27] set([0, 1, 2, 3, 4, 5, 15, 16, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31]) total number of confs: 290 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567600 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567600 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567600/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567600 Building REAL300025567601 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567601' /scratch/stefan/7901150/working/building/REAL300025567601 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567601 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567601/0 /scratch/stefan/7901150/working/building/REAL300025567601 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 98) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/98 `/scratch/stefan/7901150/working/3D/98' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC([N+](=O)[O-])=C1S(=O)(=O)NCCC1=NC(=O)O[N-]1) `REAL300025567601.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567601.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567601/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567601 none CC1=CC=CC([N+](=O)[O-])=C1S(=O)(=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', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.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, 1, 1, 8, 11, 11, 1, 14, 11, 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, 3, 3, 7, 7, 6, 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 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 3, 3, 3, 5, 24, 35, 63, 63, 63, 63, 63, 2, 2, 2, 1, 1, 1, 5, 24, 24, 35, 35] 63 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 9, 10, 25, 26, 27] set([32, 7, 8, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567601 none CC1=CC=CC([N+](=O)[O-])=C1S(=O)(=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', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.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, 1, 1, 8, 11, 11, 1, 14, 11, 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, 3, 3, 7, 7, 6, 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 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [63, 63, 63, 63, 63, 63, 63, 63, 63, 63, 52, 63, 63, 18, 8, 1, 1, 1, 1, 1, 1, 1, 63, 63, 63, 63, 63, 63, 52, 19, 19, 8, 8] 63 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: 242 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567601 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567601 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567601/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567601 Building REAL300025567602 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567602' /scratch/stefan/7901150/working/building/REAL300025567602 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567602 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567602/0 /scratch/stefan/7901150/working/building/REAL300025567602 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 99) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/99 `/scratch/stefan/7901150/working/3D/99' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2=C(F)C=C3NC(=O)CCC3=C2)[N-]O1) `REAL300025567602.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567602.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567602/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567602 none O=C1N=C(CCNS(=O)(=O)C2=C(F)C=C3NC(=O)CCC3=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 15, 1, 1, 8, 1, 11, 5, 5, 1, 1, 8, 12, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in 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, 23, 80, 135, 135, 135, 201, 201, 201, 190, 201, 201, 201, 201, 201, 201, 201, 1, 1, 9, 9, 23, 23, 80, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 22, 23] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 680 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567602 none O=C1N=C(CCNS(=O)(=O)C2=C(F)C=C3NC(=O)CCC3=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 15, 1, 1, 8, 1, 11, 5, 5, 1, 1, 8, 12, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 99, 74, 25, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 99, 99, 74, 74, 25, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 602 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567602 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567602 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567602/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567602 Building REAL300025567603 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567603' /scratch/stefan/7901150/working/building/REAL300025567603 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567603 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567603/0 /scratch/stefan/7901150/working/building/REAL300025567603 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 100) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/100 `/scratch/stefan/7901150/working/3D/100' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)C1=CC=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=C1) `REAL300025567603.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567603.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567603/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567603 none CN(C)C(=O)C1=CC=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', '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.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, 8, 5, 1, 11, 1, 1, 1, 1, 1, 14, 11, 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, 6, 7, 7, 7, 7, 7, 7, 6, 6, 4, 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, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 41, 65, 159, 159, 159, 159, 159, 1, 9, 9, 9, 9, 9, 9, 1, 1, 1, 9, 41, 41, 65, 65, 1] 201 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 37, 22, 29, 30, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36]) total number of confs: 448 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567603 none CN(C)C(=O)C1=CC=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', '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.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, 8, 5, 1, 11, 1, 1, 1, 1, 1, 14, 11, 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, 6, 7, 7, 7, 7, 7, 7, 6, 6, 4, 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, 159, 201, 159, 159, 159, 159, 127, 84, 127, 127, 24, 8, 1, 1, 1, 1, 1, 1, 1, 159, 201, 201, 201, 201, 201, 201, 159, 159, 159, 84, 24, 24, 8, 8, 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]) total number of confs: 729 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567603 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567603 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567603/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567603 Building REAL300025567604 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567604' /scratch/stefan/7901150/working/building/REAL300025567604 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567604 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567604/0 /scratch/stefan/7901150/working/building/REAL300025567604 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 101) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/101 `/scratch/stefan/7901150/working/3D/101' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2=CC=C(OC3CCCC3)C=C2)[N-]O1) `REAL300025567604.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567604.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567604/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567604 none O=C1N=C(CCNS(=O)(=O)C2=CC=C(OC3CCCC3)C=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 1, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 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, 7, 7, 7] 0 hydrogens need rotated 201 conformations in 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, 17, 52, 70, 70, 70, 70, 70, 70, 70, 164, 201, 201, 201, 201, 70, 70, 1, 1, 9, 9, 17, 17, 52, 70, 70, 201, 201, 201, 201, 201, 201, 201, 201, 201, 70, 70] 201 rigid atoms, others: [0, 1, 2, 3, 4, 22, 23] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 560 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567604 none O=C1N=C(CCNS(=O)(=O)C2=CC=C(OC3CCCC3)C=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 1, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 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, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [70, 70, 70, 25, 15, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 7, 18, 18, 18, 18, 1, 1, 70, 70, 25, 25, 15, 15, 5, 1, 1, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1] 201 rigid atoms, others: [7, 40, 41, 10, 11, 12, 13, 14, 20, 21, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 217 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567604 none O=C1N=C(CCNS(=O)(=O)C2=CC=C(OC3CCCC3)C=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 1, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 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, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 113, 80, 37, 18, 6, 18, 18, 6, 18, 18, 6, 1, 1, 1, 1, 1, 1, 18, 18, 201, 201, 113, 113, 80, 80, 37, 18, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 14, 15, 16, 17, 18, 19, 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, 29, 30, 40, 41]) total number of confs: 709 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567604 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567604 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567604/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567604 Building REAL300025567605 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567605' /scratch/stefan/7901150/working/building/REAL300025567605 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567605 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567605/0 /scratch/stefan/7901150/working/building/REAL300025567605 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 102) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/102 `/scratch/stefan/7901150/working/3D/102' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC2=CC=CN=C2C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=C1) `REAL300025567605.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567605.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567605/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567605 none CC1=CC2=CC=CN=C2C(S(=O)(=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.ar', 'N.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 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, 3, 7, 7, 7, 6, 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, 1, 7, 7, 7, 21, 74, 104, 201, 201, 201, 201, 201, 1, 2, 2, 2, 1, 1, 1, 1, 21, 74, 74, 104, 104, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 35, 22, 26, 27, 28, 29] set([32, 33, 34, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 30, 31]) total number of confs: 618 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567605 none CC1=CC2=CC=CN=C2C(S(=O)(=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.ar', 'N.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 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, 3, 7, 7, 7, 6, 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, 201, 149, 79, 149, 149, 20, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 79, 20, 20, 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]) total number of confs: 693 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567605 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567605 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567605/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567605 Building REAL300025567606 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567606' /scratch/stefan/7901150/working/building/REAL300025567606 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567606 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567606/0 /scratch/stefan/7901150/working/building/REAL300025567606 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 103) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/103 `/scratch/stefan/7901150/working/3D/103' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CCOC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1) `REAL300025567606.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567606.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567606/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567606 none CC(C)CCOC1=CC=C(S(=O)(=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', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 14, 11, 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, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 9, 5, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 24, 34, 71, 71, 71, 71, 71, 1, 1, 9, 9, 9, 9, 9, 9, 9, 8, 8, 5, 5, 1, 1, 9, 24, 24, 34, 34, 1, 1] 201 rigid atoms, others: [35, 36, 5, 6, 7, 8, 9, 10, 43, 22, 23, 42] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41]) total number of confs: 246 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567606 none CC(C)CCOC1=CC=C(S(=O)(=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', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 14, 11, 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, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 124, 124, 71, 46, 71, 71, 46, 36, 46, 46, 12, 8, 1, 1, 1, 1, 1, 1, 1, 71, 71, 201, 201, 201, 201, 201, 201, 201, 201, 201, 124, 124, 71, 71, 36, 13, 13, 8, 8, 71, 71] 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: 899 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567606 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567606 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567606/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567606 Building REAL300025567607 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567607' /scratch/stefan/7901150/working/building/REAL300025567607 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567607 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567607/0 /scratch/stefan/7901150/working/building/REAL300025567607 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 104) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/104 `/scratch/stefan/7901150/working/3D/104' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)COC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1) `REAL300025567607.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567607.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567607/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567607 none COC(=O)COC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 5, 12, 1, 1, 1, 1, 14, 11, 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, 3, 7, 7, 7, 7, 7, 6, 6, 4, 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: [31, 31, 7, 30, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 25, 35, 79, 79, 79, 79, 79, 1, 1, 31, 30, 30, 7, 7, 1, 1, 9, 25, 25, 35, 35, 1, 1] 201 rigid atoms, others: [36, 5, 6, 7, 8, 9, 10, 22, 23, 29, 30, 37] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35]) total number of confs: 307 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567607 none COC(=O)COC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 5, 12, 1, 1, 1, 1, 14, 11, 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, 3, 7, 7, 7, 7, 7, 6, 6, 4, 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, 141, 201, 119, 79, 49, 79, 79, 49, 39, 49, 49, 14, 8, 1, 1, 1, 1, 1, 1, 1, 79, 79, 201, 201, 201, 141, 141, 79, 79, 39, 15, 15, 8, 8, 79, 79] 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: 841 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567607 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567607 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567607/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567607 Building REAL300025567608 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567608' /scratch/stefan/7901150/working/building/REAL300025567608 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567608 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567608/0 /scratch/stefan/7901150/working/building/REAL300025567608 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 105) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/105 `/scratch/stefan/7901150/working/3D/105' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C(C(F)(F)F)=C1) `REAL300025567608.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567608.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567608/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567608 none N#CC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C(C(F)(F)F)=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 5, 15, 15, 15, 1, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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 117 conformations in input total number of sets (complete confs): 117 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 29, 55, 117, 117, 117, 117, 117, 1, 1, 2, 2, 2, 1, 1, 1, 5, 29, 29, 55, 55, 1] 117 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 18, 19, 23, 24, 25, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 26, 27, 28, 29, 30]) total number of confs: 353 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567608 none N#CC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C(C(F)(F)F)=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 5, 15, 15, 15, 1, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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 117 conformations in input total number of sets (complete confs): 117 using faster count positions algorithm for large data unique positions, atoms: [117, 117, 117, 117, 117, 117, 85, 117, 117, 24, 8, 1, 1, 1, 1, 1, 1, 1, 113, 117, 117, 117, 117, 117, 117, 117, 85, 24, 24, 8, 8, 117] 117 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]) total number of confs: 467 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567608 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567608 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567608/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567608 Building REAL300025567609 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567609' /scratch/stefan/7901150/working/building/REAL300025567609 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567609 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567609/0 /scratch/stefan/7901150/working/building/REAL300025567609 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 106) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/106 `/scratch/stefan/7901150/working/3D/106' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2=CC=C(OCC3CCCCC3)C=C2)[N-]O1) `REAL300025567609.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567609.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567609/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567609 none O=C1N=C(CCNS(=O)(=O)C2=CC=C(OCC3CCCCC3)C=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 5, 5, 1, 1, 8, 12, 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: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in 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, 13, 36, 46, 46, 46, 46, 46, 46, 46, 95, 95, 201, 201, 201, 201, 201, 46, 46, 1, 1, 9, 9, 13, 13, 36, 46, 46, 95, 95, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 46, 46] 201 rigid atoms, others: [0, 1, 2, 3, 4, 24, 25] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 574 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567609 none O=C1N=C(CCNS(=O)(=O)C2=CC=C(OCC3CCCCC3)C=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 5, 5, 1, 1, 8, 12, 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: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [46, 46, 46, 21, 15, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 6, 8, 21, 21, 21, 21, 21, 1, 1, 46, 46, 21, 21, 15, 15, 5, 1, 1, 8, 8, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1] 201 rigid atoms, others: [32, 7, 10, 11, 12, 13, 14, 47, 46, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 192 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567609 none O=C1N=C(CCNS(=O)(=O)C2=CC=C(OCC3CCCCC3)C=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 5, 5, 1, 1, 8, 12, 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: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 108, 85, 41, 21, 21, 21, 21, 21, 21, 21, 12, 6, 1, 1, 1, 1, 1, 1, 1, 21, 21, 201, 201, 108, 108, 85, 85, 41, 21, 21, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21] 201 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 46, 47]) total number of confs: 621 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567609 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567609 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567609/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567609 Building REAL300025567610 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567610' /scratch/stefan/7901150/working/building/REAL300025567610 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567610 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567610/0 /scratch/stefan/7901150/working/building/REAL300025567610 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 107) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/107 `/scratch/stefan/7901150/working/3D/107' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(Cl)C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=C1Cl) `REAL300025567610.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567610.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567610/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567610 none CC1=CC=C(Cl)C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 16, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 1, 11, 11, 11, 19, 78, 109, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 1, 1, 19, 78, 78, 109, 109] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 24, 25] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 26, 27, 28, 29, 30]) total number of confs: 659 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567610 none CC1=CC=C(Cl)C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 16, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 105, 201, 201, 201, 105, 67, 105, 105, 19, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 189, 201, 67, 20, 20, 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: 1019 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567610 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567610 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567610/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567610 Building REAL300025567611 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567611' /scratch/stefan/7901150/working/building/REAL300025567611 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567611 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567611/0 /scratch/stefan/7901150/working/building/REAL300025567611 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 108) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/108 `/scratch/stefan/7901150/working/3D/108' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(S(C)(=O)=O)C=C1S(=O)(=O)NCCC1=NC(=O)O[N-]1) `REAL300025567611.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567611.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567611/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567611 none CC1=CC=C(S(C)(=O)=O)C=C1S(=O)(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', '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, 1, 1, 1, 14, 5, 11, 11, 1, 1, 14, 11, 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, 3, 3, 7, 7, 7, 6, 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, 2, 2, 2, 1, 1, 1, 5, 5, 5, 11, 41, 67, 155, 155, 155, 155, 155, 2, 2, 2, 1, 1, 3, 3, 3, 1, 11, 43, 43, 67, 67] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 9, 10, 11, 26, 27, 31] set([6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 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 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567611 none CC1=CC=C(S(C)(=O)=O)C=C1S(=O)(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', '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, 1, 1, 1, 14, 5, 11, 11, 1, 1, 14, 11, 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, 3, 3, 7, 7, 7, 6, 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: [155, 155, 155, 125, 155, 155, 201, 201, 201, 155, 125, 84, 125, 125, 24, 8, 1, 1, 1, 1, 1, 1, 1, 155, 155, 155, 155, 125, 201, 201, 201, 155, 84, 24, 24, 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: 893 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567611 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567611 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567611/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567611 Building REAL300025567612 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567612' /scratch/stefan/7901150/working/building/REAL300025567612 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567612 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567612/0 /scratch/stefan/7901150/working/building/REAL300025567612 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 109) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/109 `/scratch/stefan/7901150/working/3D/109' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2=CC=CC3=CN=CC=C32)[N-]O1) `REAL300025567612.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567612/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567612 none O=C1N=C(CCNS(=O)(=O)C2=CC=CC3=CN=CC=C32)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 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, 9, 25, 75, 130, 130, 130, 134, 134, 134, 134, 134, 134, 134, 134, 134, 1, 1, 9, 9, 25, 25, 75, 134, 134, 134, 134, 134, 134] 134 rigid atoms, others: [0, 1, 2, 3, 4, 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, 32]) total number of confs: 558 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567612 none O=C1N=C(CCNS(=O)(=O)C2=CC=CC3=CN=CC=C32)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 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, 54, 31, 9, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 134, 134, 54, 54, 31, 31, 9, 1, 1, 1, 1, 1, 1] 134 rigid atoms, others: [32, 7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 362 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567612 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567612 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567612/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567612 Building REAL300025567613 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567613' /scratch/stefan/7901150/working/building/REAL300025567613 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567613 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567613/0 /scratch/stefan/7901150/working/building/REAL300025567613 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 110) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/110 `/scratch/stefan/7901150/working/3D/110' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2=CC=C([N+](=O)[O-])C=C2Cl)[N-]O1) `REAL300025567613.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567613.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567613/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567613 none O=C1N=C(CCNS(=O)(=O)C2=CC=C([N+](=O)[O-])C=C2Cl)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 16, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 3, 3, 7, 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: [1, 1, 1, 1, 1, 9, 25, 89, 130, 130, 130, 134, 134, 134, 134, 134, 134, 134, 134, 134, 1, 1, 9, 9, 25, 25, 89, 134, 134, 134] 134 rigid atoms, others: [0, 1, 2, 3, 4, 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]) total number of confs: 514 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567613 none O=C1N=C(CCNS(=O)(=O)C2=CC=C([N+](=O)[O-])C=C2Cl)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 16, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 3, 3, 7, 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: [134, 134, 134, 60, 39, 9, 5, 1, 5, 5, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 134, 134, 60, 60, 39, 39, 9, 1, 1, 1] 134 rigid atoms, others: [7, 10, 11, 12, 13, 14, 17, 18, 19, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 15, 16, 20, 21, 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 /scratch/stefan/7901150/working/building/REAL300025567613 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567613 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567613/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567613 Building REAL300025567614 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567614' /scratch/stefan/7901150/working/building/REAL300025567614 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567614 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567614/0 /scratch/stefan/7901150/working/building/REAL300025567614 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 111) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/111 `/scratch/stefan/7901150/working/3D/111' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C2=CC=CN=C2C=C1) `REAL300025567614.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567614.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567614/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567614 none CC1=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C2=CC=CN=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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.ar', '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, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 8, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 104 conformations in input total number of sets (complete confs): 104 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 5, 5, 5, 7, 31, 48, 104, 104, 104, 104, 104, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 31, 31, 48, 48, 1, 1, 1, 1, 1] 104 rigid atoms, others: [0, 1, 2, 3, 33, 35, 32, 34, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 311 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567614 none CC1=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C2=CC=CN=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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.ar', '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, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 8, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 104 conformations in input total number of sets (complete confs): 104 using faster count positions algorithm for large data unique positions, atoms: [104, 104, 80, 60, 80, 80, 21, 8, 1, 1, 1, 1, 1, 1, 1, 104, 104, 104, 104, 104, 104, 104, 104, 104, 104, 104, 60, 22, 22, 8, 8, 104, 104, 104, 104, 104] 104 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: 362 number of broken/clashed sets: 38 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567614 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567614 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567614/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567614 Building REAL300025567615 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567615' /scratch/stefan/7901150/working/building/REAL300025567615 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567615 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567615/0 /scratch/stefan/7901150/working/building/REAL300025567615 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 112) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/112 `/scratch/stefan/7901150/working/3D/112' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CCOC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1) `REAL300025567615.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567615.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567615/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567615 none COC(=O)CCOC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 11, 5, 5, 12, 1, 1, 1, 1, 14, 11, 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, 5, 7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 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, 33, 14, 33, 5, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 19, 27, 63, 63, 63, 63, 63, 1, 1, 33, 33, 33, 13, 13, 5, 5, 1, 1, 7, 19, 19, 27, 27, 1, 1] 201 rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 40, 23, 24, 39] set([0, 1, 2, 3, 4, 5, 12, 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: 290 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567615 none COC(=O)CCOC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 11, 5, 5, 12, 1, 1, 1, 1, 14, 11, 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, 5, 7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 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, 143, 201, 76, 72, 63, 47, 63, 63, 47, 39, 47, 47, 12, 8, 1, 1, 1, 1, 1, 1, 1, 63, 63, 201, 201, 201, 143, 143, 76, 76, 63, 63, 39, 13, 13, 8, 8, 63, 63] 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: 864 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567615 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567615 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567615/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567615 Building REAL300025567616 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567616' /scratch/stefan/7901150/working/building/REAL300025567616 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025567616 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567616/0 /scratch/stefan/7901150/working/building/REAL300025567616 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 113) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/113 `/scratch/stefan/7901150/working/3D/113' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2=C(Br)C=CS2)[N-]O1) `REAL300025567616.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567616.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567616/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567616 none O=C1N=C(CCNS(=O)(=O)C2=C(Br)C=CS2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'S.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 17, 1, 1, 14, 8, 12, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 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: [1, 1, 1, 1, 1, 9, 25, 100, 169, 169, 169, 201, 201, 201, 201, 201, 1, 1, 9, 9, 25, 25, 100, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 16, 17] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 696 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567616 none O=C1N=C(CCNS(=O)(=O)C2=C(Br)C=CS2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'S.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 17, 1, 1, 14, 8, 12, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 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: [201, 201, 201, 99, 63, 19, 8, 1, 8, 8, 1, 1, 1, 1, 1, 1, 201, 201, 99, 99, 63, 63, 19, 1, 1] 201 rigid atoms, others: [7, 10, 11, 12, 13, 14, 15, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 16, 17, 18, 19, 20, 21, 22]) total number of confs: 610 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567616 /scratch/stefan/7901150/working /scratch/stefan/7901150 mkdir: created directory `1' /scratch/stefan/7901150/working/building/REAL300025567616/1 /scratch/stefan/7901150/working/building/REAL300025567616 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 1 (index: 114) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/114 `/scratch/stefan/7901150/working/3D/114' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CC[N-]S(=O)(=O)C2=C(Br)C=CS2)[N-]O1) `REAL300025567616.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025567616.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567616/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567616 none O=C1N=C(CC[N-]S(=O)(=O)C2=C(Br)C=CS2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'S.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 17, 1, 1, 14, 8, 12, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 3, 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, 1, 9, 11, 40, 108, 108, 108, 157, 157, 157, 157, 157, 1, 1, 9, 9, 11, 11, 157, 157] 157 rigid atoms, others: [0, 1, 2, 3, 4, 16, 17] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23]) total number of confs: 466 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567616 none O=C1N=C(CC[N-]S(=O)(=O)C2=C(Br)C=CS2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'S.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 17, 1, 1, 14, 8, 12, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 157 conformations in input total number of sets (complete confs): 157 using faster count positions algorithm for large data unique positions, atoms: [157, 157, 157, 86, 86, 33, 12, 1, 12, 12, 1, 1, 1, 1, 1, 1, 157, 157, 86, 86, 86, 86, 1, 1] 157 rigid atoms, others: [7, 10, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 16, 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 /scratch/stefan/7901150/working/building/REAL300025567616 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567616 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 1: /scratch/stefan/7901150/working/building/REAL300025567616/1.* 0: /scratch/stefan/7901150/working/building/REAL300025567616/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567616 Building REAL300025567617 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567617' /scratch/stefan/7901150/working/building/REAL300025567617 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567617 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567617/0 /scratch/stefan/7901150/working/building/REAL300025567617 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 115) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/115 `/scratch/stefan/7901150/working/3D/115' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCN(S(=O)(=O)NCCC2=NC(=O)O[N-]2)CC1) `REAL300025567617.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567617/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567617 none CC(C)(C)OC(=O)N1CCN(S(=O)(=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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 5, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 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, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 17, 45, 51, 115, 115, 115, 115, 115, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 17, 45, 45, 51, 51, 1, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 5, 7, 8, 9, 10, 11, 44, 45, 46, 43, 23, 24, 37] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42]) total number of confs: 365 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567617 none CC(C)(C)OC(=O)N1CCN(S(=O)(=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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 5, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 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, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations 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, 115, 175, 115, 115, 115, 83, 51, 83, 83, 18, 8, 1, 1, 1, 1, 1, 1, 1, 115, 115, 201, 201, 201, 201, 201, 201, 201, 201, 201, 115, 115, 115, 115, 51, 18, 18, 8, 8, 115, 115, 115, 115] 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]) total number of confs: 684 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567617 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567617 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567617/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567617 Building REAL300025567618 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567618' /scratch/stefan/7901150/working/building/REAL300025567618 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567618 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567618/0 /scratch/stefan/7901150/working/building/REAL300025567618 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 116) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/116 `/scratch/stefan/7901150/working/3D/116' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCCC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1) `REAL300025567618.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567618.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567618/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567618 none CC(=O)NCCC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 1, 11, 8, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 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, 11, 11, 5, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 29, 43, 114, 114, 114, 114, 114, 1, 1, 12, 12, 12, 11, 5, 5, 3, 3, 1, 1, 8, 29, 29, 43, 43, 1, 1] 201 rigid atoms, others: [32, 33, 5, 6, 7, 8, 9, 10, 39, 40, 22, 23] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38]) total number of confs: 339 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567618 none CC(=O)NCCC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 1, 11, 8, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 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, 199, 119, 89, 89, 114, 114, 89, 70, 89, 89, 22, 8, 1, 1, 1, 1, 1, 1, 1, 114, 114, 201, 201, 201, 201, 199, 199, 119, 119, 114, 114, 70, 23, 23, 8, 8, 114, 114] 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: 1039 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567618 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567618 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567618/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567618 Building REAL300025567619 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567619' /scratch/stefan/7901150/working/building/REAL300025567619 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567619 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567619/0 /scratch/stefan/7901150/working/building/REAL300025567619 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 117) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/117 `/scratch/stefan/7901150/working/3D/117' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2=CC=C([N+](=O)[O-])C=C2F)[N-]O1) `REAL300025567619.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567619.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567619/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567619 none O=C1N=C(CCNS(=O)(=O)C2=CC=C([N+](=O)[O-])C=C2F)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 3, 3, 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: [1, 1, 1, 1, 1, 9, 25, 92, 143, 143, 143, 201, 201, 190, 201, 201, 201, 201, 201, 201, 1, 1, 9, 9, 25, 25, 92, 201, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 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]) total number of confs: 696 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567619 none O=C1N=C(CCNS(=O)(=O)C2=CC=C([N+](=O)[O-])C=C2F)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 3, 3, 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: [201, 201, 201, 97, 71, 23, 7, 1, 7, 7, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 201, 201, 97, 97, 71, 71, 23, 1, 1, 1] 201 rigid atoms, others: [7, 10, 11, 12, 13, 14, 17, 18, 19, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 15, 16, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 598 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567619 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567619 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567619/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567619 Building REAL300025567620 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567620' /scratch/stefan/7901150/working/building/REAL300025567620 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025567620 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567620/0 /scratch/stefan/7901150/working/building/REAL300025567620 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 118) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/118 `/scratch/stefan/7901150/working/3D/118' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2=CC(Br)=CN=C2Cl)[N-]O1) `REAL300025567620.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567620.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567620/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567620 none O=C1N=C(CCNS(=O)(=O)C2=CC(Br)=CN=C2Cl)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 17, 1, 8, 1, 16, 8, 12, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 3, 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: [1, 1, 1, 1, 1, 9, 21, 101, 184, 184, 184, 201, 201, 201, 201, 201, 201, 201, 1, 1, 9, 9, 21, 21, 101, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 18, 19] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 742 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567620 none O=C1N=C(CCNS(=O)(=O)C2=CC(Br)=CN=C2Cl)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 17, 1, 8, 1, 16, 8, 12, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 3, 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: [201, 201, 201, 89, 61, 15, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 89, 89, 61, 61, 15, 1, 1] 201 rigid atoms, others: [7, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 560 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567620 /scratch/stefan/7901150/working /scratch/stefan/7901150 mkdir: created directory `1' /scratch/stefan/7901150/working/building/REAL300025567620/1 /scratch/stefan/7901150/working/building/REAL300025567620 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 1 (index: 119) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/119 `/scratch/stefan/7901150/working/3D/119' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CC[N-]S(=O)(=O)C2=CC(Br)=CN=C2Cl)[N-]O1) `REAL300025567620.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025567620.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567620/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567620 none O=C1N=C(CC[N-]S(=O)(=O)C2=CC(Br)=CN=C2Cl)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 17, 1, 8, 1, 16, 8, 12, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 60 conformations in input total number of sets (complete confs): 60 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 9, 9, 27, 54, 54, 54, 60, 60, 60, 60, 60, 60, 60, 1, 1, 9, 9, 9, 9, 60, 60] 60 rigid atoms, others: [0, 1, 2, 3, 4, 18, 19] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567620 none O=C1N=C(CC[N-]S(=O)(=O)C2=CC(Br)=CN=C2Cl)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 17, 1, 8, 1, 16, 8, 12, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 60 conformations in input total number of sets (complete confs): 60 using faster count positions algorithm for large data unique positions, atoms: [60, 60, 60, 27, 27, 12, 6, 1, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 60, 60, 27, 27, 27, 27, 1, 1] 60 rigid atoms, others: [7, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 18, 19, 20, 21, 22, 23]) total number of confs: 146 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567620 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567620 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 1: /scratch/stefan/7901150/working/building/REAL300025567620/1.* 0: /scratch/stefan/7901150/working/building/REAL300025567620/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567620 Building REAL300025567621 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567621' /scratch/stefan/7901150/working/building/REAL300025567621 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567621 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567621/0 /scratch/stefan/7901150/working/building/REAL300025567621 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 120) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/120 `/scratch/stefan/7901150/working/3D/120' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(CNC(C)=O)C=C1S(=O)(=O)NCCC1=NC(=O)O[N-]1) `REAL300025567621.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567621.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567621/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567621 none COC1=CC=C(CNC(C)=O)C=C1S(=O)(=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.3', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', '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, 12, 1, 1, 1, 1, 5, 8, 1, 5, 11, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 6, 6, 4, 7, 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, 6, 23, 23, 23, 1, 1, 1, 7, 7, 7, 11, 39, 39, 125, 125, 125, 125, 125, 3, 3, 3, 1, 1, 6, 6, 23, 23, 23, 23, 1, 11, 39, 39, 39, 39] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 11, 12, 13, 36, 28, 29] set([0, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41]) total number of confs: 327 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567621 none COC1=CC=C(CNC(C)=O)C=C1S(=O)(=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.3', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', '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, 12, 1, 1, 1, 1, 5, 8, 1, 5, 11, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 6, 6, 4, 7, 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: [131, 125, 125, 125, 95, 125, 125, 183, 201, 201, 201, 125, 87, 53, 87, 87, 8, 8, 1, 1, 1, 1, 1, 1, 1, 131, 131, 131, 125, 125, 183, 183, 201, 201, 201, 201, 125, 53, 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]) total number of confs: 885 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567621 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567621 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567621/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567621 Building REAL300025567622 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567622' /scratch/stefan/7901150/working/building/REAL300025567622 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567622 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567622/0 /scratch/stefan/7901150/working/building/REAL300025567622 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 121) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/121 `/scratch/stefan/7901150/working/3D/121' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2=CC=C(C3=CC=CC=C3)C=C2)[N-]O1) `REAL300025567622.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567622.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567622/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567622 none O=C1N=C(CCNS(=O)(=O)C2=CC=C(C3=CC=CC=C3)C=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 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, 1, 9, 25, 109, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 9, 9, 25, 25, 109, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 22, 23] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 796 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567622 none O=C1N=C(CCNS(=O)(=O)C2=CC=C(C3=CC=CC=C3)C=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 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: [201, 201, 201, 54, 27, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 3, 3, 1, 3, 3, 1, 1, 201, 201, 54, 54, 27, 27, 5, 1, 1, 3, 3, 2, 3, 3, 1, 1] 201 rigid atoms, others: [36, 37, 7, 10, 11, 12, 13, 14, 20, 21, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35]) 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567622 none O=C1N=C(CCNS(=O)(=O)C2=CC=C(C3=CC=CC=C3)C=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 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: [201, 201, 201, 94, 52, 9, 3, 1, 3, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 201, 201, 94, 94, 52, 52, 9, 3, 3, 1, 1, 1, 1, 1, 3, 3] 201 rigid atoms, others: [32, 33, 34, 35, 13, 14, 15, 16, 17, 18, 19, 31] 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, 36, 37]) total number of confs: 575 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567622 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567622 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567622/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567622 Building REAL300025567623 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567623' /scratch/stefan/7901150/working/building/REAL300025567623 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567623 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567623/0 /scratch/stefan/7901150/working/building/REAL300025567623 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 122) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/122 `/scratch/stefan/7901150/working/3D/122' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2=CC=C([N+](=O)[O-])C(Br)=C2)[N-]O1) `REAL300025567623.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567623.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567623/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567623 none O=C1N=C(CCNS(=O)(=O)C2=CC=C([N+](=O)[O-])C(Br)=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'Br', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 11, 11, 1, 17, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 3, 3, 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: [1, 1, 1, 1, 1, 9, 25, 80, 109, 109, 109, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 9, 9, 25, 25, 80, 201, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 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]) total number of confs: 610 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567623 none O=C1N=C(CCNS(=O)(=O)C2=CC=C([N+](=O)[O-])C(Br)=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'Br', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 11, 11, 1, 17, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 3, 3, 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: [201, 201, 201, 87, 51, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 87, 87, 51, 51, 9, 1, 1, 1] 201 rigid atoms, others: [7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 544 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567623 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567623 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567623/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567623 Building REAL300025567624 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567624' /scratch/stefan/7901150/working/building/REAL300025567624 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567624 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567624/0 /scratch/stefan/7901150/working/building/REAL300025567624 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 123) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/123 `/scratch/stefan/7901150/working/3D/123' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCNC(=O)C1=CC=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=C1) `REAL300025567624.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567624.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567624/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567624 none C=CCNC(=O)C1=CC=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.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: [1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 4, 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: [35, 11, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 33, 42, 127, 127, 127, 127, 127, 1, 35, 35, 35, 11, 11, 5, 1, 1, 1, 9, 33, 33, 42, 42, 1] 201 rigid atoms, others: [32, 4, 38, 6, 7, 8, 9, 10, 11, 23, 30, 31] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37]) total number of confs: 400 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567624 none C=CCNC(=O)C1=CC=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.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: [1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 4, 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, 151, 151, 127, 151, 127, 127, 127, 127, 92, 69, 92, 92, 18, 7, 1, 1, 1, 1, 1, 1, 1, 127, 201, 201, 201, 201, 201, 151, 127, 127, 127, 69, 19, 19, 7, 7, 127] 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: 759 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567624 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567624 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567624/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567624 Building REAL300025567625 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567625' /scratch/stefan/7901150/working/building/REAL300025567625 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567625 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567625/0 /scratch/stefan/7901150/working/building/REAL300025567625 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 124) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/124 `/scratch/stefan/7901150/working/3D/124' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C(C)=C1) `REAL300025567625.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567625.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567625/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567625 none COC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.3', '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, 14, 11, 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, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 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, 5, 5, 5, 9, 34, 58, 201, 201, 201, 201, 201, 1, 1, 1, 3, 3, 3, 1, 1, 9, 34, 34, 58, 58, 2, 2, 2, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 34, 18, 19, 20, 24, 25] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 463 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567625 none COC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.3', '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, 14, 11, 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, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 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, 102, 201, 201, 24, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 102, 24, 25, 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]) total number of confs: 800 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567625 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567625 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567625/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567625 Building REAL300025567626 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567626' /scratch/stefan/7901150/working/building/REAL300025567626 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567626 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567626/0 /scratch/stefan/7901150/working/building/REAL300025567626 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 125) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/125 `/scratch/stefan/7901150/working/3D/125' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C)=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1C) `REAL300025567626.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567626.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567626/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567626 none COC1=CC(C)=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 12, 1, 1, 1, 5, 1, 14, 11, 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, 3, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 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, 3, 3, 3, 5, 27, 57, 199, 199, 199, 199, 199, 1, 1, 1, 4, 4, 4, 1, 2, 2, 2, 5, 27, 27, 57, 57, 1, 2, 2, 2] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 34, 19, 20, 21, 25] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37]) total number of confs: 476 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567626 none COC1=CC(C)=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 12, 1, 1, 1, 5, 1, 14, 11, 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, 3, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 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, 199, 199, 199, 199, 199, 199, 104, 199, 199, 24, 8, 1, 1, 1, 1, 1, 1, 1, 199, 199, 199, 201, 201, 201, 199, 199, 199, 199, 104, 25, 25, 8, 8, 199, 199, 199, 199] 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: 779 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567626 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567626 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567626/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567626 Building REAL300025567627 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567627' /scratch/stefan/7901150/working/building/REAL300025567627 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567627 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567627/0 /scratch/stefan/7901150/working/building/REAL300025567627 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 126) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/126 `/scratch/stefan/7901150/working/3D/126' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC1)C1=CC=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=C1) `REAL300025567627.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567627.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567627/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567627 none O=C(NC1CC1)C1=CC=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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: [11, 1, 8, 5, 5, 5, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 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: [6, 6, 1, 1, 1, 1, 6, 18, 18, 13, 18, 18, 24, 24, 24, 60, 109, 117, 201, 201, 201, 201, 201, 18, 6, 1, 1, 1, 1, 1, 18, 18, 18, 60, 109, 109, 117, 117, 18] 201 rigid atoms, others: [2, 3, 4, 5, 25, 26, 27, 28, 29] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 608 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567627 none O=C(NC1CC1)C1=CC=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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: [11, 1, 8, 5, 5, 5, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 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: [6, 1, 6, 6, 18, 18, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 36, 51, 152, 152, 152, 152, 152, 1, 6, 18, 18, 18, 18, 18, 1, 1, 1, 9, 36, 36, 51, 51, 1] 201 rigid atoms, others: [32, 1, 38, 6, 7, 8, 9, 10, 11, 23, 30, 31] set([0, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37]) 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567627 none O=C(NC1CC1)C1=CC=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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: [11, 1, 8, 5, 5, 5, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 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: [190, 152, 190, 190, 201, 201, 152, 152, 152, 152, 111, 81, 111, 111, 22, 8, 1, 1, 1, 1, 1, 1, 1, 152, 190, 201, 201, 201, 201, 201, 152, 152, 152, 81, 22, 23, 8, 8, 152] 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: 681 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567627 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567627 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567627/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567627 Building REAL300025567628 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567628' /scratch/stefan/7901150/working/building/REAL300025567628 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025567628 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567628/0 /scratch/stefan/7901150/working/building/REAL300025567628 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 127) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/127 `/scratch/stefan/7901150/working/3D/127' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2=CC=CC(F)=C2[N+](=O)[O-])[N-]O1) `REAL300025567628.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567628.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567628/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567628 none O=C1N=C(CCNS(=O)(=O)C2=CC=CC(F)=C2[N+](=O)[O-])[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 94 conformations in input total number of sets (complete confs): 94 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 9, 23, 68, 94, 94, 94, 94, 94, 94, 94, 94, 94, 94, 94, 94, 1, 1, 9, 9, 23, 23, 68, 94, 94, 94] 94 rigid atoms, others: [0, 1, 2, 3, 4, 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]) total number of confs: 378 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567628 none O=C1N=C(CCNS(=O)(=O)C2=CC=CC(F)=C2[N+](=O)[O-])[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 94 conformations in input total number of sets (complete confs): 94 using faster count positions algorithm for large data unique positions, atoms: [94, 94, 94, 44, 28, 5, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 94, 94, 44, 44, 28, 28, 5, 1, 1, 1] 94 rigid atoms, others: [7, 10, 11, 12, 13, 14, 15, 16, 17, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 283 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567628 /scratch/stefan/7901150/working /scratch/stefan/7901150 mkdir: created directory `1' /scratch/stefan/7901150/working/building/REAL300025567628/1 /scratch/stefan/7901150/working/building/REAL300025567628 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 1 (index: 128) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/128 `/scratch/stefan/7901150/working/3D/128' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CC[N-]S(=O)(=O)C2=CC=CC(F)=C2[N+](=O)[O-])[N-]O1) `REAL300025567628.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025567628.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567628/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567628 none O=C1N=C(CC[N-]S(=O)(=O)C2=CC=CC(F)=C2[N+](=O)[O-])[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 9, 11, 28, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 1, 1, 9, 9, 11, 11, 46, 46, 46] 46 rigid atoms, others: [0, 1, 2, 3, 4, 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]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567628 none O=C1N=C(CC[N-]S(=O)(=O)C2=CC=CC(F)=C2[N+](=O)[O-])[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 15, 1, 8, 11, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [46, 46, 46, 22, 21, 5, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 46, 46, 22, 22, 21, 21, 1, 1, 1] 46 rigid atoms, others: [7, 10, 11, 12, 13, 14, 15, 16, 17, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 121 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567628 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567628 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 1: /scratch/stefan/7901150/working/building/REAL300025567628/1.* 0: /scratch/stefan/7901150/working/building/REAL300025567628/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567628 Building REAL300025567629 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567629' /scratch/stefan/7901150/working/building/REAL300025567629 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567629 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567629/0 /scratch/stefan/7901150/working/building/REAL300025567629 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 129) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/129 `/scratch/stefan/7901150/working/3D/129' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC(F)(F)F)C1=CC=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=C1) `REAL300025567629.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567629.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567629/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567629 none O=C(NCC(F)(F)F)C1=CC=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 15, 15, 15, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 1, 7, 7, 19, 19, 19, 19, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 35, 41, 98, 98, 98, 98, 98, 1, 7, 19, 19, 1, 1, 1, 9, 35, 35, 41, 41, 1] 201 rigid atoms, others: [1, 37, 8, 9, 10, 11, 12, 13, 25, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 32, 33, 34, 35, 36]) total number of confs: 319 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567629 none O=C(NCC(F)(F)F)C1=CC=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 15, 15, 15, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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: [139, 98, 139, 139, 201, 201, 201, 201, 98, 98, 98, 98, 75, 57, 75, 75, 15, 7, 1, 1, 1, 1, 1, 1, 1, 98, 139, 201, 201, 98, 98, 98, 57, 15, 15, 7, 7, 98] 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: 771 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567629 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567629 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567629/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567629 Building REAL300025567630 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567630' /scratch/stefan/7901150/working/building/REAL300025567630 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567630 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567630/0 /scratch/stefan/7901150/working/building/REAL300025567630 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 130) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/130 `/scratch/stefan/7901150/working/3D/130' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C1=C(C)NN=C1S(=O)(=O)NCCC1=NC(=O)O[N-]1) `REAL300025567630.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567630.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567630/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567630 none CCOC(=O)C1=C(C)NN=C1S(=O)(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', '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, 12, 1, 11, 1, 1, 5, 8, 8, 1, 14, 11, 11, 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: [7, 7, 3, 7, 5, 7, 7, 7, 4, 7, 7, 7, 6, 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: [16, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 13, 39, 60, 156, 156, 156, 156, 156, 16, 16, 16, 16, 16, 2, 2, 2, 1, 13, 39, 39, 60, 60] 201 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 11, 31] set([0, 1, 2, 4, 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: 477 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567630 none CCOC(=O)C1=C(C)NN=C1S(=O)(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', '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, 12, 1, 11, 1, 1, 5, 8, 8, 1, 14, 11, 11, 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: [7, 7, 3, 7, 5, 7, 7, 7, 4, 7, 7, 7, 6, 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, 189, 189, 156, 189, 156, 156, 156, 156, 156, 97, 50, 97, 97, 15, 9, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 156, 156, 156, 156, 50, 15, 15, 9, 9] 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: 697 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567630 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567630 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567630/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567630 Building REAL300025567631 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567631' /scratch/stefan/7901150/working/building/REAL300025567631 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567631 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567631/0 /scratch/stefan/7901150/working/building/REAL300025567631 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 131) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/131 `/scratch/stefan/7901150/working/3D/131' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2=C(Cl)N=C3C=CC=CN32)[N-]O1) `REAL300025567631.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567631.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567631/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567631 none O=C1N=C(CCNS(=O)(=O)C2=C(Cl)N=C3C=CC=CN32)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'Cl', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 16, 8, 1, 1, 1, 1, 1, 8, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 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: [1, 1, 1, 1, 1, 9, 25, 81, 124, 124, 124, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 9, 9, 25, 25, 81, 201, 201, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 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]) total number of confs: 614 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567631 none O=C1N=C(CCNS(=O)(=O)C2=C(Cl)N=C3C=CC=CN32)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'Cl', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 16, 8, 1, 1, 1, 1, 1, 8, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 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: [201, 201, 201, 104, 88, 23, 11, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 104, 104, 88, 88, 23, 1, 1, 1, 1] 201 rigid atoms, others: [7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 603 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567631 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567631 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567631/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567631 Building REAL300025567632 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567632' /scratch/stefan/7901150/working/building/REAL300025567632 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567632 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567632/0 /scratch/stefan/7901150/working/building/REAL300025567632 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 132) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/132 `/scratch/stefan/7901150/working/3D/132' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)N1CCN(S(=O)(=O)NCCC2=NC(=O)O[N-]2)CC1) `REAL300025567632.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567632.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567632/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567632 none CCOC(=O)N1CCN(S(=O)(=O)NCCC2=NC(=O)O[N-]2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 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, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 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, 4, 2, 1, 2, 1, 1, 1, 1, 1, 6, 6, 6, 17, 47, 55, 125, 125, 125, 125, 125, 1, 1, 9, 9, 9, 8, 8, 1, 1, 1, 1, 17, 47, 47, 55, 55, 1, 1, 1, 1] 201 rigid atoms, others: [3, 5, 6, 7, 8, 9, 39, 40, 37, 21, 22, 38, 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, 32, 33, 34, 35, 36]) total number of confs: 373 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567632 none CCOC(=O)N1CCN(S(=O)(=O)NCCC2=NC(=O)O[N-]2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 5, 12, 1, 11, 8, 5, 5, 8, 14, 11, 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, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 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, 191, 189, 125, 189, 125, 125, 125, 81, 45, 81, 81, 17, 7, 1, 1, 1, 1, 1, 1, 1, 125, 125, 201, 201, 201, 201, 201, 125, 125, 125, 125, 45, 18, 18, 7, 7, 125, 125, 125, 125] 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: 730 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567632 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567632 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567632/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567632 Building REAL300025567633 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567633' /scratch/stefan/7901150/working/building/REAL300025567633 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567633 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567633/0 /scratch/stefan/7901150/working/building/REAL300025567633 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 133) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/133 `/scratch/stefan/7901150/working/3D/133' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)C2CCC1(CS(=O)(=O)NCCC1=NC(=O)O[N-]1)C(=O)C2) `REAL300025567633.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567633.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567633/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567633 none CC1(C)C2CCC1(CS(=O)(=O)NCCC1=NC(=O)O[N-]1)C(=O)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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: [1, 1, 1, 1, 1, 1, 1, 1, 4, 8, 8, 8, 21, 77, 117, 201, 201, 201, 201, 201, 1, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 4, 4, 21, 77, 77, 117, 117, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 41, 42, 7, 20, 21, 22, 33, 29, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 661 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567633 none CC1(C)C2CCC1(CS(=O)(=O)NCCC1=NC(=O)O[N-]1)C(=O)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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: [201, 201, 201, 201, 201, 201, 201, 147, 101, 147, 147, 24, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 101, 24, 25, 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, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 844 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567633 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567633 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567633/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567633 Building REAL300025567634 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567634' /scratch/stefan/7901150/working/building/REAL300025567634 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 3 protomers extracted for REAL300025567634 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567634/0 /scratch/stefan/7901150/working/building/REAL300025567634 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 134) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/134 `/scratch/stefan/7901150/working/3D/134' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2CC[N@H+](CC3=CC=CC=C3)C2)[N-]O1) `REAL300025567634.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567634/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567634 none O=C1N=C(CCNS(=O)(=O)C2CC[N@H+](CC3=CC=CC=C3)C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 5, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 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 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 7, 12, 12, 14, 14, 14, 14, 14, 14, 14, 14, 17, 17, 17, 17, 17, 17, 14, 1, 1, 7, 7, 12, 12, 12, 14, 14, 14, 14, 14, 17, 17, 17, 17, 17, 17, 17, 14, 14] 17 rigid atoms, others: [0, 1, 2, 3, 4, 23, 24] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567634 none O=C1N=C(CCNS(=O)(=O)C2CC[N@H+](CC3=CC=CC=C3)C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 5, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 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 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 6, 6, 6, 4, 1, 4, 4, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 1, 14, 14, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 1, 1] 17 rigid atoms, others: [32, 33, 34, 43, 7, 10, 11, 12, 13, 14, 15, 22, 42, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 41 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567634 none O=C1N=C(CCNS(=O)(=O)C2CC[N@H+](CC3=CC=CC=C3)C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 5, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 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 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 10, 10, 10, 7, 3, 7, 7, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 3, 17, 17, 10, 10, 10, 10, 10, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3] 17 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 13, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43]) total number of confs: 47 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567634 /scratch/stefan/7901150/working /scratch/stefan/7901150 mkdir: created directory `1' /scratch/stefan/7901150/working/building/REAL300025567634/1 /scratch/stefan/7901150/working/building/REAL300025567634 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 1 (index: 135) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/135 `/scratch/stefan/7901150/working/3D/135' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2CC[N@@H+](CC3=CC=CC=C3)C2)[N-]O1) `REAL300025567634.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025567634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567634/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567634 none O=C1N=C(CCNS(=O)(=O)C2CC[N@@H+](CC3=CC=CC=C3)C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 5, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 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 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 8, 13, 17, 22, 22, 22, 24, 24, 24, 24, 24, 27, 27, 27, 27, 27, 27, 24, 1, 1, 8, 8, 13, 13, 17, 24, 24, 24, 24, 24, 27, 27, 27, 27, 27, 27, 27, 24, 24] 27 rigid atoms, others: [0, 1, 2, 3, 4, 23, 24] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567634 none O=C1N=C(CCNS(=O)(=O)C2CC[N@@H+](CC3=CC=CC=C3)C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 5, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 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 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 24, 11, 11, 10, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 1, 24, 24, 11, 11, 11, 11, 10, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 1, 1] 27 rigid atoms, others: [32, 33, 34, 43, 7, 10, 11, 12, 13, 14, 15, 22, 42, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 73 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567634 none O=C1N=C(CCNS(=O)(=O)C2CC[N@@H+](CC3=CC=CC=C3)C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 5, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 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 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 18, 18, 16, 9, 4, 9, 9, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 4, 27, 27, 18, 18, 18, 18, 16, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4] 27 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 13, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43]) total number of confs: 85 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567634 /scratch/stefan/7901150/working /scratch/stefan/7901150 mkdir: created directory `2' /scratch/stefan/7901150/working/building/REAL300025567634/2 /scratch/stefan/7901150/working/building/REAL300025567634 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 2 (index: 136) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/136 `/scratch/stefan/7901150/working/3D/136' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2CCN(CC3=CC=CC=C3)C2)[N-]O1) `REAL300025567634.mol2' -> `2.mol2' `temp.mol2' -> `REAL300025567634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567634/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567634 none O=C1N=C(CCNS(=O)(=O)C2CCN(CC3=CC=CC=C3)C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 9, 23, 54, 92, 92, 92, 131, 131, 131, 131, 201, 201, 201, 201, 201, 201, 131, 1, 1, 9, 9, 23, 23, 54, 131, 131, 131, 131, 131, 201, 201, 201, 201, 201, 201, 201, 131, 131] 201 rigid atoms, others: [0, 1, 2, 3, 4, 22, 23] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 922 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567634 none O=C1N=C(CCNS(=O)(=O)C2CCN(CC3=CC=CC=C3)C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [131, 131, 131, 55, 44, 19, 7, 1, 7, 7, 1, 1, 1, 1, 1, 5, 8, 8, 7, 8, 8, 1, 131, 131, 55, 55, 44, 44, 19, 1, 1, 1, 1, 1, 5, 5, 8, 8, 8, 8, 8, 1, 1] 201 rigid atoms, others: [32, 33, 7, 41, 10, 11, 12, 13, 14, 42, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 377 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567634 none O=C1N=C(CCNS(=O)(=O)C2CCN(CC3=CC=CC=C3)C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 120, 107, 56, 31, 8, 31, 31, 8, 8, 8, 3, 1, 1, 1, 1, 1, 1, 1, 8, 201, 201, 120, 120, 107, 107, 56, 8, 8, 8, 8, 8, 3, 3, 1, 1, 1, 1, 1, 8, 8] 201 rigid atoms, others: [36, 37, 38, 39, 40, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42]) total number of confs: 653 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567634 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567634 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 1: /scratch/stefan/7901150/working/building/REAL300025567634/1.* 2: /scratch/stefan/7901150/working/building/REAL300025567634/2.* 0: /scratch/stefan/7901150/working/building/REAL300025567634/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567634 Building REAL300025567635 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567635' /scratch/stefan/7901150/working/building/REAL300025567635 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567635 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567635/0 /scratch/stefan/7901150/working/building/REAL300025567635 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 137) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/137 `/scratch/stefan/7901150/working/3D/137' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C2=C(C=CC=C2)C2=C1C=CC(S(=O)(=O)NCCC1=NC(=O)O[N-]1)=C2) `REAL300025567635.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567635.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567635/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567635 none CN1C2=C(C=CC=C2)C2=C1C=CC(S(=O)(=O)NCCC1=NC(=O)O[N-]1)=C2 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 11, 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, 7, 7, 7, 7, 7, 7, 6, 6, 4, 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, 1, 1, 1, 3, 3, 3, 9, 57, 103, 201, 201, 201, 201, 201, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 9, 57, 57, 103, 103, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 25, 29, 30, 31, 32, 33, 34, 40] set([35, 36, 37, 38, 39, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28]) total number of confs: 621 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567635 none CN1C2=C(C=CC=C2)C2=C1C=CC(S(=O)(=O)NCCC1=NC(=O)O[N-]1)=C2 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 11, 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, 7, 7, 7, 7, 7, 7, 6, 6, 4, 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, 201, 201, 201, 130, 83, 130, 130, 24, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 83, 24, 24, 8, 8, 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]) total number of confs: 656 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567635 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567635 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567635/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567635 Building REAL300025567636 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567636' /scratch/stefan/7901150/working/building/REAL300025567636 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025567636 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567636/0 /scratch/stefan/7901150/working/building/REAL300025567636 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 138) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/138 `/scratch/stefan/7901150/working/3D/138' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2=CC(Br)=CC=C2[N+](=O)[O-])[N-]O1) `REAL300025567636.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567636.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567636/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567636 none O=C1N=C(CCNS(=O)(=O)C2=CC(Br)=CC=C2[N+](=O)[O-])[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 17, 1, 1, 1, 8, 11, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 94 conformations in input total number of sets (complete confs): 94 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 9, 23, 79, 94, 94, 94, 94, 94, 94, 94, 94, 94, 94, 94, 94, 1, 1, 9, 9, 23, 23, 79, 94, 94, 94] 94 rigid atoms, others: [0, 1, 2, 3, 4, 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]) total number of confs: 332 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567636 none O=C1N=C(CCNS(=O)(=O)C2=CC(Br)=CC=C2[N+](=O)[O-])[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 17, 1, 1, 1, 8, 11, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 94 conformations in input total number of sets (complete confs): 94 using faster count positions algorithm for large data unique positions, atoms: [94, 94, 94, 47, 31, 5, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 94, 94, 47, 47, 31, 31, 5, 1, 1, 1] 94 rigid atoms, others: [7, 10, 11, 12, 13, 14, 15, 16, 17, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 283 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567636 /scratch/stefan/7901150/working /scratch/stefan/7901150 mkdir: created directory `1' /scratch/stefan/7901150/working/building/REAL300025567636/1 /scratch/stefan/7901150/working/building/REAL300025567636 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 1 (index: 139) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/139 `/scratch/stefan/7901150/working/3D/139' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CC[N-]S(=O)(=O)C2=CC(Br)=CC=C2[N+](=O)[O-])[N-]O1) `REAL300025567636.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025567636.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567636/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567636 none O=C1N=C(CC[N-]S(=O)(=O)C2=CC(Br)=CC=C2[N+](=O)[O-])[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 17, 1, 1, 1, 8, 11, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 52 conformations in input total number of sets (complete confs): 52 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 9, 15, 34, 52, 52, 52, 52, 52, 52, 52, 52, 52, 52, 52, 52, 1, 1, 9, 9, 15, 15, 52, 52, 52] 52 rigid atoms, others: [0, 1, 2, 3, 4, 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]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567636 none O=C1N=C(CC[N-]S(=O)(=O)C2=CC(Br)=CC=C2[N+](=O)[O-])[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 17, 1, 1, 1, 8, 11, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 52 conformations in input total number of sets (complete confs): 52 using faster count positions algorithm for large data unique positions, atoms: [52, 52, 52, 26, 21, 5, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 52, 52, 26, 26, 21, 21, 1, 1, 1] 52 rigid atoms, others: [7, 10, 11, 12, 13, 14, 15, 16, 17, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 150 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567636 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567636 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 1: /scratch/stefan/7901150/working/building/REAL300025567636/1.* 0: /scratch/stefan/7901150/working/building/REAL300025567636/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567636 Building REAL300025567637 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567637' /scratch/stefan/7901150/working/building/REAL300025567637 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567637 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567637/0 /scratch/stefan/7901150/working/building/REAL300025567637 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 140) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/140 `/scratch/stefan/7901150/working/3D/140' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)S1) `REAL300025567637.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567637.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567637/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567637 none COC(=O)C1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)S1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 12, 1, 11, 1, 1, 1, 1, 14, 11, 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, 3, 7, 5, 7, 7, 7, 7, 7, 6, 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, 3, 1, 3, 1, 1, 1, 1, 1, 6, 6, 6, 23, 62, 84, 154, 154, 154, 154, 154, 1, 3, 3, 3, 1, 1, 23, 62, 62, 84, 84] 201 rigid atoms, others: [2, 4, 5, 6, 7, 8, 20, 24, 25] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 26, 27, 28, 29, 30]) total number of confs: 511 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567637 none COC(=O)C1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)S1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 12, 1, 11, 1, 1, 1, 1, 14, 11, 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, 3, 7, 5, 7, 7, 7, 7, 7, 6, 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, 154, 201, 154, 154, 154, 73, 47, 73, 73, 16, 6, 1, 1, 1, 1, 1, 1, 1, 154, 201, 201, 201, 154, 154, 47, 16, 16, 6, 6] 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: 605 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567637 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567637 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567637/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567637 Building REAL300025567638 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567638' /scratch/stefan/7901150/working/building/REAL300025567638 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567638 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567638/0 /scratch/stefan/7901150/working/building/REAL300025567638 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 141) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/141 `/scratch/stefan/7901150/working/3D/141' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)C1=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=CC=C1F) `REAL300025567638.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567638.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567638/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567638 none CS(=O)(=O)C1=CC(S(=O)(=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', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 14, 11, 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, 6, 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, 3, 3, 3, 9, 44, 64, 182, 182, 182, 182, 182, 1, 1, 1, 1, 7, 7, 7, 1, 9, 44, 44, 64, 64, 1, 1] 201 rigid atoms, others: [32, 1, 33, 4, 5, 6, 7, 19, 20, 21, 22, 26] set([0, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 27, 28, 29, 30, 31]) total number of confs: 465 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567638 none CS(=O)(=O)C1=CC(S(=O)(=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', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 14, 11, 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, 6, 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, 182, 201, 201, 182, 182, 129, 93, 129, 129, 24, 8, 1, 1, 1, 1, 1, 1, 1, 182, 182, 182, 182, 201, 201, 201, 182, 93, 24, 24, 8, 8, 182, 182] 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: 719 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567638 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567638 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567638/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567638 Building REAL300025567639 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567639' /scratch/stefan/7901150/working/building/REAL300025567639 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567639 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567639/0 /scratch/stefan/7901150/working/building/REAL300025567639 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 142) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/142 `/scratch/stefan/7901150/working/3D/142' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC([N+](=O)[O-])=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1C) `REAL300025567639.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567639.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567639/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567639 none CC1=CC([N+](=O)[O-])=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [5, 1, 1, 1, 8, 11, 11, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 6, 6, 4, 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 105 conformations in input total number of sets (complete confs): 105 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 3, 3, 3, 5, 29, 47, 105, 105, 105, 105, 105, 1, 1, 1, 2, 2, 2, 1, 5, 29, 29, 47, 47, 1, 2, 2, 2] 105 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 32, 20, 21, 22, 26] set([5, 6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 27, 28, 29, 30, 31, 33, 34, 35]) total number of confs: 319 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567639 none CC1=CC([N+](=O)[O-])=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [5, 1, 1, 1, 8, 11, 11, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 6, 6, 4, 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 105 conformations in input total number of sets (complete confs): 105 using faster count positions algorithm for large data unique positions, atoms: [105, 105, 105, 105, 105, 105, 105, 105, 80, 105, 105, 22, 8, 1, 1, 1, 1, 1, 1, 1, 105, 105, 105, 105, 105, 105, 105, 80, 22, 22, 8, 8, 105, 105, 105, 105] 105 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: 397 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567639 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567639 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567639/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567639 Building REAL300025567640 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567640' /scratch/stefan/7901150/working/building/REAL300025567640 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567640 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567640/0 /scratch/stefan/7901150/working/building/REAL300025567640 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 143) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/143 `/scratch/stefan/7901150/working/3D/143' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2=CC=CC3=C2COC3=O)[N-]O1) `REAL300025567640.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567640.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567640/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567640 none O=C1N=C(CCNS(=O)(=O)C2=CC=CC3=C2COC3=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 5, 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: [1, 1, 1, 1, 1, 9, 25, 106, 179, 179, 179, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 9, 9, 25, 25, 106, 201, 201, 201, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 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: 723 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567640 none O=C1N=C(CCNS(=O)(=O)C2=CC=CC3=C2COC3=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 5, 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, 201, 201, 90, 57, 13, 4, 1, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 90, 90, 59, 59, 13, 1, 1, 1, 1, 1] 201 rigid atoms, others: [7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 20, 21, 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 /scratch/stefan/7901150/working/building/REAL300025567640 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567640 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567640/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567640 Building REAL300025567641 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567641' /scratch/stefan/7901150/working/building/REAL300025567641 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025567641 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567641/0 /scratch/stefan/7901150/working/building/REAL300025567641 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 144) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/144 `/scratch/stefan/7901150/working/3D/144' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CC[N-]S(=O)(=O)C2=C(F)C=C(F)C=C2F)[N-]O1) `REAL300025567641.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567641.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567641/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567641 none O=C1N=C(CC[N-]S(=O)(=O)C2=C(F)C=C(F)C=C2F)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 15, 1, 1, 15, 1, 1, 15, 8, 12, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [1, 1, 1, 1, 1, 9, 13, 42, 99, 99, 99, 117, 117, 117, 105, 117, 117, 117, 117, 1, 1, 9, 9, 13, 13, 117, 117] 117 rigid atoms, others: [0, 1, 2, 3, 4, 19, 20] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 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 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567641 none O=C1N=C(CC[N-]S(=O)(=O)C2=C(F)C=C(F)C=C2F)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 15, 1, 1, 15, 1, 1, 15, 8, 12, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 117 conformations in input total number of sets (complete confs): 117 using faster count positions algorithm for large data unique positions, atoms: [117, 117, 117, 69, 69, 21, 8, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 117, 117, 69, 69, 69, 69, 1, 1] 117 rigid atoms, others: [7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 19, 20, 21, 22, 23, 24]) total number of confs: 314 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567641 /scratch/stefan/7901150/working /scratch/stefan/7901150 mkdir: created directory `1' /scratch/stefan/7901150/working/building/REAL300025567641/1 /scratch/stefan/7901150/working/building/REAL300025567641 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 1 (index: 145) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/145 `/scratch/stefan/7901150/working/3D/145' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2=C(F)C=C(F)C=C2F)[N-]O1) `REAL300025567641.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025567641.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567641/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567641 none O=C1N=C(CCNS(=O)(=O)C2=C(F)C=C(F)C=C2F)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 15, 1, 1, 15, 1, 1, 15, 8, 12, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 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: [1, 1, 1, 1, 1, 9, 25, 106, 176, 176, 176, 201, 201, 201, 176, 201, 201, 201, 201, 1, 1, 9, 9, 25, 25, 106, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 19, 20] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 826 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567641 none O=C1N=C(CCNS(=O)(=O)C2=C(F)C=C(F)C=C2F)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 15, 1, 1, 15, 1, 1, 15, 8, 12, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 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: [201, 201, 201, 107, 83, 24, 11, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 107, 107, 83, 83, 24, 1, 1] 201 rigid atoms, others: [7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 607 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567641 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567641 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 1: /scratch/stefan/7901150/working/building/REAL300025567641/1.* 0: /scratch/stefan/7901150/working/building/REAL300025567641/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567641 Building REAL300025567642 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567642' /scratch/stefan/7901150/working/building/REAL300025567642 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567642 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567642/0 /scratch/stefan/7901150/working/building/REAL300025567642 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 146) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/146 `/scratch/stefan/7901150/working/3D/146' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCCC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)S1) `REAL300025567642.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567642.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567642/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567642 none CC(=O)NCCC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 1, 11, 8, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 14, 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, 7, 7, 7, 6, 6, 4, 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: [18, 18, 18, 7, 4, 1, 1, 1, 1, 1, 1, 7, 7, 7, 9, 29, 42, 116, 116, 116, 116, 116, 1, 18, 18, 18, 18, 7, 7, 4, 4, 1, 1, 9, 29, 29, 42, 42] 201 rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 22, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 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 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567642 none CC(=O)NCCC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 1, 11, 8, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 14, 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, 7, 7, 7, 6, 6, 4, 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, 191, 152, 116, 116, 116, 116, 52, 46, 52, 52, 12, 8, 1, 1, 1, 1, 1, 1, 1, 116, 201, 201, 201, 201, 191, 191, 152, 152, 116, 116, 46, 12, 12, 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: 766 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567642 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567642 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567642/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567642 Building REAL300025567643 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567643' /scratch/stefan/7901150/working/building/REAL300025567643 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567643 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567643/0 /scratch/stefan/7901150/working/building/REAL300025567643 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 147) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/147 `/scratch/stefan/7901150/working/3D/147' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CCN(CCC(C)C)S(=O)(=O)NCCC1=NC(=O)O[N-]1) `REAL300025567643.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567643.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567643/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567643 none CC(C)CCN(CCC(C)C)S(=O)(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', '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, 8, 5, 5, 5, 5, 5, 14, 11, 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, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [167, 167, 167, 167, 120, 76, 120, 179, 179, 179, 179, 49, 76, 76, 16, 8, 1, 1, 1, 1, 1, 1, 1, 167, 167, 167, 167, 167, 167, 167, 167, 167, 167, 167, 179, 179, 179, 179, 179, 179, 179, 179, 179, 179, 179, 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, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 1046 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567643 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567643 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567643/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567643 Building REAL300025567644 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567644' /scratch/stefan/7901150/working/building/REAL300025567644 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567644 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567644/0 /scratch/stefan/7901150/working/building/REAL300025567644 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 148) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/148 `/scratch/stefan/7901150/working/3D/148' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC(C)C1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)S1) `REAL300025567644.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567644.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567644/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567644 none CC(=O)NC(C)C1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 1, 11, 8, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 14, 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, 7, 7, 7, 6, 6, 4, 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, 12, 12, 11, 1, 11, 1, 1, 1, 1, 1, 6, 6, 6, 22, 58, 71, 157, 157, 157, 157, 157, 1, 12, 12, 12, 12, 11, 11, 11, 11, 1, 1, 22, 58, 58, 71, 71] 201 rigid atoms, others: [32, 4, 6, 7, 8, 9, 10, 22, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37]) total number of confs: 486 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567644 none CC(=O)NC(C)C1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 1, 11, 8, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 14, 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, 7, 7, 7, 6, 6, 4, 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, 157, 201, 157, 157, 157, 78, 54, 78, 78, 19, 8, 1, 1, 1, 1, 1, 1, 1, 157, 201, 201, 201, 201, 201, 201, 201, 201, 157, 157, 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, 33, 34, 35, 36, 37]) total number of confs: 675 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567644 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567644 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567644/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567644 Building REAL300025567645 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567645' /scratch/stefan/7901150/working/building/REAL300025567645 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567645 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567645/0 /scratch/stefan/7901150/working/building/REAL300025567645 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 149) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/149 `/scratch/stefan/7901150/working/3D/149' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2=CN=C3NC=CC=C23)[N-]O1) `REAL300025567645.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567645.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567645/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567645 none O=C1N=C(CCNS(=O)(=O)C2=CN=C3NC=CC=C23)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 8, 1, 8, 1, 1, 1, 1, 8, 12, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 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: [1, 1, 1, 1, 1, 9, 23, 78, 141, 141, 141, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 9, 9, 23, 23, 78, 201, 201, 201, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 19, 20] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 664 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567645 none O=C1N=C(CCNS(=O)(=O)C2=CN=C3NC=CC=C23)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 8, 1, 8, 1, 1, 1, 1, 8, 12, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 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: [201, 201, 201, 106, 75, 23, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 106, 106, 75, 75, 23, 1, 1, 1, 1, 1] 201 rigid atoms, others: [7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 625 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567645 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567645 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567645/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567645 Building REAL300025567646 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567646' /scratch/stefan/7901150/working/building/REAL300025567646 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567646 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567646/0 /scratch/stefan/7901150/working/building/REAL300025567646 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 150) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/150 `/scratch/stefan/7901150/working/3D/150' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C(F)C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=C1) `REAL300025567646.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567646.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567646/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567646 none COC(=O)C1=CC=C(F)C(S(=O)(=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', 'C.ar', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 1, 15, 1, 14, 11, 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, 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, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 21, 58, 70, 151, 151, 151, 151, 151, 1, 7, 7, 7, 1, 1, 21, 58, 58, 70, 70, 1] 201 rigid atoms, others: [33, 2, 4, 5, 6, 7, 8, 9, 10, 22, 26, 27] set([0, 1, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 28, 29, 30, 31, 32]) total number of confs: 452 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567646 none COC(=O)C1=CC=C(F)C(S(=O)(=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', 'C.ar', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 1, 15, 1, 14, 11, 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, 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, 151, 201, 151, 151, 151, 151, 151, 95, 63, 95, 95, 18, 8, 1, 1, 1, 1, 1, 1, 1, 151, 201, 201, 201, 151, 151, 63, 18, 18, 8, 8, 151] 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: 671 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567646 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567646 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567646/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567646 Building REAL300025567647 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567647' /scratch/stefan/7901150/working/building/REAL300025567647 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567647 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567647/0 /scratch/stefan/7901150/working/building/REAL300025567647 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 151) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/151 `/scratch/stefan/7901150/working/3D/151' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C(C)C=C1S(=O)(=O)NCCC1=NC(=O)O[N-]1) `REAL300025567647.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567647.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567647/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567647 none CCOC1=CC=C(C)C=C1S(=O)(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', '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, 12, 1, 1, 1, 1, 5, 1, 1, 14, 11, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 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: [13, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 14, 42, 64, 168, 168, 168, 168, 168, 13, 13, 13, 13, 13, 1, 1, 2, 2, 2, 1, 14, 42, 42, 64, 64] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 8, 9, 10, 27, 28] set([0, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 33, 34, 35, 36, 37]) total number of confs: 484 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567647 none CCOC1=CC=C(C)C=C1S(=O)(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', '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, 12, 1, 1, 1, 1, 5, 1, 1, 14, 11, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 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, 168, 168, 168, 164, 168, 168, 168, 135, 90, 135, 135, 22, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 168, 168, 168, 168, 168, 168, 90, 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]) total number of confs: 665 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567647 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567647 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567647/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567647 Building REAL300025567648 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567648' /scratch/stefan/7901150/working/building/REAL300025567648 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567648 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567648/0 /scratch/stefan/7901150/working/building/REAL300025567648 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 152) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/152 `/scratch/stefan/7901150/working/3D/152' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2=CC=C(F)C(C(F)(F)F)=C2)[N-]O1) `REAL300025567648.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567648.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567648/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567648 none O=C1N=C(CCNS(=O)(=O)C2=CC=C(F)C(C(F)(F)F)=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 15, 1, 5, 15, 15, 15, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 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 201 conformations in 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, 25, 78, 114, 114, 114, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 9, 9, 25, 25, 78, 201, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 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]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567648 none O=C1N=C(CCNS(=O)(=O)C2=CC=C(F)C(C(F)(F)F)=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 15, 1, 5, 15, 15, 15, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 93, 57, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 201, 201, 93, 93, 57, 57, 9, 1, 1, 1] 201 rigid atoms, others: [7, 10, 11, 12, 13, 14, 15, 16, 20, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 581 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567648 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567648 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567648/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567648 Building REAL300025567649 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567649' /scratch/stefan/7901150/working/building/REAL300025567649 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567649 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567649/0 /scratch/stefan/7901150/working/building/REAL300025567649 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 153) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/153 `/scratch/stefan/7901150/working/3D/153' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)C(=O)C1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1) `REAL300025567649.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567649.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567649/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567649 none CCN(CC)C(=O)C1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.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, 5, 8, 5, 5, 1, 11, 1, 1, 1, 1, 14, 11, 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, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 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, 6, 4, 6, 7, 1, 4, 1, 1, 1, 1, 1, 2, 2, 2, 8, 27, 44, 109, 109, 109, 109, 109, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 8, 27, 27, 44, 44, 1, 1] 201 rigid atoms, others: [35, 36, 5, 7, 8, 9, 10, 11, 43, 23, 24, 42] set([0, 1, 2, 3, 4, 6, 12, 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: 328 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567649 none CCN(CC)C(=O)C1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.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, 5, 8, 5, 5, 1, 11, 1, 1, 1, 1, 14, 11, 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, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 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: [177, 117, 117, 117, 177, 109, 117, 75, 109, 109, 75, 49, 75, 75, 17, 7, 1, 1, 1, 1, 1, 1, 1, 109, 109, 177, 177, 177, 177, 177, 177, 177, 177, 177, 177, 109, 109, 49, 17, 17, 7, 7, 109, 109] 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: 1295 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567649 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567649 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567649/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567649 Building REAL300025567650 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567650' /scratch/stefan/7901150/working/building/REAL300025567650 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567650 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567650/0 /scratch/stefan/7901150/working/building/REAL300025567650 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 154) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/154 `/scratch/stefan/7901150/working/3D/154' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCOC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1) `REAL300025567650.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567650.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567650/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567650 none CCCCCOC1=CC=C(S(=O)(=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', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 14, 11, 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, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 12, 5, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 20, 28, 60, 60, 60, 60, 60, 1, 1, 12, 12, 12, 11, 11, 12, 12, 11, 11, 5, 5, 1, 1, 8, 20, 20, 28, 28, 1, 1] 201 rigid atoms, others: [35, 36, 5, 6, 7, 8, 9, 10, 43, 22, 23, 42] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41]) total number of confs: 220 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567650 none CCCCCOC1=CC=C(S(=O)(=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', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 14, 11, 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, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 103, 60, 44, 60, 60, 44, 37, 44, 44, 12, 8, 1, 1, 1, 1, 1, 1, 1, 60, 60, 201, 201, 201, 201, 201, 201, 201, 201, 201, 107, 107, 60, 60, 37, 13, 13, 8, 8, 60, 60] 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: 815 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567650 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567650 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567650/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567650 Building REAL300025567651 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567651' /scratch/stefan/7901150/working/building/REAL300025567651 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025567651 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567651/0 /scratch/stefan/7901150/working/building/REAL300025567651 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 155) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/155 `/scratch/stefan/7901150/working/3D/155' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2=C(Cl)C=CC=C2[N+](=O)[O-])[N-]O1) `REAL300025567651.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567651.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567651/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567651 none O=C1N=C(CCNS(=O)(=O)C2=C(Cl)C=CC=C2[N+](=O)[O-])[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 16, 1, 1, 1, 1, 8, 11, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 9, 23, 66, 73, 73, 73, 73, 73, 73, 73, 73, 73, 73, 73, 73, 1, 1, 9, 9, 23, 23, 66, 73, 73, 73] 73 rigid atoms, others: [0, 1, 2, 3, 4, 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]) total number of confs: 258 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567651 none O=C1N=C(CCNS(=O)(=O)C2=C(Cl)C=CC=C2[N+](=O)[O-])[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 16, 1, 1, 1, 1, 8, 11, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [73, 73, 73, 37, 27, 5, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 73, 73, 37, 37, 27, 27, 5, 1, 1, 1] 73 rigid atoms, others: [7, 10, 11, 12, 13, 14, 15, 16, 17, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 216 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567651 /scratch/stefan/7901150/working /scratch/stefan/7901150 mkdir: created directory `1' /scratch/stefan/7901150/working/building/REAL300025567651/1 /scratch/stefan/7901150/working/building/REAL300025567651 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 1 (index: 156) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/156 `/scratch/stefan/7901150/working/3D/156' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CC[N-]S(=O)(=O)C2=C(Cl)C=CC=C2[N+](=O)[O-])[N-]O1) `REAL300025567651.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025567651.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567651/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567651 none O=C1N=C(CC[N-]S(=O)(=O)C2=C(Cl)C=CC=C2[N+](=O)[O-])[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 16, 1, 1, 1, 1, 8, 11, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 3, 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: [1, 1, 1, 1, 1, 9, 14, 32, 51, 51, 51, 51, 51, 51, 51, 51, 51, 51, 51, 51, 1, 1, 9, 9, 14, 14, 51, 51, 51] 51 rigid atoms, others: [0, 1, 2, 3, 4, 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]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567651 none O=C1N=C(CC[N-]S(=O)(=O)C2=C(Cl)C=CC=C2[N+](=O)[O-])[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 16, 1, 1, 1, 1, 8, 11, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [51, 51, 51, 19, 17, 5, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 51, 51, 19, 19, 17, 17, 1, 1, 1] 51 rigid atoms, others: [7, 10, 11, 12, 13, 14, 15, 16, 17, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 126 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567651 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567651 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 1: /scratch/stefan/7901150/working/building/REAL300025567651/1.* 0: /scratch/stefan/7901150/working/building/REAL300025567651/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567651 Building REAL300025567652 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567652' /scratch/stefan/7901150/working/building/REAL300025567652 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567652 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567652/0 /scratch/stefan/7901150/working/building/REAL300025567652 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 157) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/157 `/scratch/stefan/7901150/working/3D/157' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2=CC=CC(N3C=NN=N3)=C2)[N-]O1) `REAL300025567652.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567652/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567652 none O=C1N=C(CCNS(=O)(=O)C2=CC=CC(N3C=NN=N3)=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 8, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 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 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 9, 17, 33, 45, 45, 45, 51, 51, 51, 51, 51, 55, 55, 55, 55, 51, 1, 1, 9, 9, 17, 17, 33, 51, 51, 51, 55, 51] 55 rigid atoms, others: [0, 1, 2, 3, 4, 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]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567652 none O=C1N=C(CCNS(=O)(=O)C2=CC=CC(N3C=NN=N3)=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 8, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 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 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [51, 51, 51, 19, 19, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 1, 51, 51, 19, 19, 19, 19, 9, 1, 1, 1, 3, 1] 55 rigid atoms, others: [32, 7, 10, 11, 12, 13, 14, 15, 20, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 126 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567652 none O=C1N=C(CCNS(=O)(=O)C2=CC=CC(N3C=NN=N3)=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 8, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 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 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [55, 55, 55, 23, 23, 13, 5, 3, 5, 5, 3, 2, 3, 3, 1, 1, 1, 1, 1, 1, 3, 55, 55, 23, 23, 23, 23, 13, 2, 3, 3, 1, 3] 55 rigid atoms, others: [14, 15, 16, 17, 18, 19, 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, 29, 30, 32]) total number of confs: 143 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567652 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567652 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567652/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567652 Building REAL300025567653 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567653' /scratch/stefan/7901150/working/building/REAL300025567653 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567653 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567653/0 /scratch/stefan/7901150/working/building/REAL300025567653 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 158) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/158 `/scratch/stefan/7901150/working/3D/158' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C2=CC=CC=C12) `REAL300025567653.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567653.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567653/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567653 none CCOC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C2=CC=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 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, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 7, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 23, 43, 130, 130, 130, 130, 130, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 18, 1, 1, 5, 23, 23, 43, 43, 1, 1, 1, 1] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 40, 39, 19, 20, 21, 22, 23, 24, 38, 37, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36]) total number of confs: 366 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567653 none CCOC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C2=CC=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 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, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 130, 130, 130, 130, 130, 84, 130, 130, 24, 8, 1, 1, 1, 1, 1, 1, 1, 130, 130, 130, 130, 130, 130, 201, 201, 201, 201, 201, 130, 130, 84, 24, 24, 8, 8, 130, 130, 130, 130] 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: 648 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567653 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567653 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567653/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567653 Building REAL300025567654 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567654' /scratch/stefan/7901150/working/building/REAL300025567654 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567654 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567654/0 /scratch/stefan/7901150/working/building/REAL300025567654 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 159) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/159 `/scratch/stefan/7901150/working/3D/159' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2=CC=C(SC(F)(F)F)C=C2)[N-]O1) `REAL300025567654.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567654.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567654/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567654 none O=C1N=C(CCNS(=O)(=O)C2=CC=C(SC(F)(F)F)C=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 14, 5, 15, 15, 15, 1, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 6, 9, 9, 11, 11, 11, 11, 11, 11, 11, 15, 15, 15, 15, 11, 11, 1, 1, 6, 6, 9, 9, 9, 11, 11, 11, 11] 15 rigid atoms, others: [0, 1, 2, 3, 4, 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]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567654 none O=C1N=C(CCNS(=O)(=O)C2=CC=C(SC(F)(F)F)C=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 14, 5, 15, 15, 15, 1, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [11, 11, 11, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 8, 8, 8, 1, 1, 11, 11, 5, 5, 5, 5, 5, 1, 1, 1, 1] 15 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 46 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567654 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567654 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567654/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567654 Building REAL300025567655 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567655' /scratch/stefan/7901150/working/building/REAL300025567655 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567655 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567655/0 /scratch/stefan/7901150/working/building/REAL300025567655 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 160) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/160 `/scratch/stefan/7901150/working/3D/160' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2=CN=CC(Br)=C2)[N-]O1) `REAL300025567655.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567655.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567655/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567655 none O=C1N=C(CCNS(=O)(=O)C2=CN=CC(Br)=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 8, 1, 1, 17, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 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: [1, 1, 1, 1, 1, 9, 25, 80, 122, 122, 122, 201, 201, 201, 201, 201, 201, 1, 1, 9, 9, 25, 25, 80, 201, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 17, 18] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 656 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567655 none O=C1N=C(CCNS(=O)(=O)C2=CN=CC(Br)=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 8, 1, 1, 17, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 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: [201, 201, 201, 95, 55, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 201, 201, 95, 95, 55, 55, 9, 1, 1, 1] 201 rigid atoms, others: [7, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 17, 18, 19, 20, 21, 22, 23]) total number of confs: 576 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567655 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567655 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567655/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567655 Building REAL300025567656 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567656' /scratch/stefan/7901150/working/building/REAL300025567656 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567656 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567656/0 /scratch/stefan/7901150/working/building/REAL300025567656 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 161) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/161 `/scratch/stefan/7901150/working/3D/161' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)NC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1) `REAL300025567656.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567656/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567656 none CS(=O)(=O)NC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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: [5, 14, 11, 11, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 6, 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 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 6, 6, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 13, 13, 13, 13, 13, 1, 1, 6, 6, 6, 4, 1, 1, 8, 8, 8, 8, 8, 1, 1] 16 rigid atoms, others: [34, 35, 4, 5, 6, 7, 8, 9, 21, 22, 27, 28] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 29, 30, 31, 32, 33]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567656 none CS(=O)(=O)NC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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: [5, 14, 11, 11, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 6, 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 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 13, 9, 13, 13, 9, 5, 9, 9, 5, 3, 1, 1, 1, 1, 1, 1, 1, 13, 13, 16, 16, 16, 16, 13, 13, 5, 5, 5, 3, 3, 13, 13] 16 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: 86 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567656 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567656 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567656/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567656 Building REAL300025567657 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567657' /scratch/stefan/7901150/working/building/REAL300025567657 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567657 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567657/0 /scratch/stefan/7901150/working/building/REAL300025567657 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 162) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/162 `/scratch/stefan/7901150/working/3D/162' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCCOC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1) `REAL300025567657.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567657.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567657/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567657 none CCOCCOC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 12, 5, 5, 12, 1, 1, 1, 1, 14, 11, 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, 3, 7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 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: [20, 20, 10, 5, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 20, 29, 80, 80, 80, 80, 80, 1, 1, 20, 20, 20, 20, 20, 10, 10, 5, 5, 1, 1, 7, 20, 20, 29, 29, 1, 1] 201 rigid atoms, others: [33, 34, 5, 6, 7, 8, 9, 10, 40, 41, 22, 23] set([0, 1, 2, 3, 4, 11, 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: 253 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567657 none CCOCCOC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 12, 5, 5, 12, 1, 1, 1, 1, 14, 11, 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, 3, 7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 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, 185, 157, 150, 80, 55, 80, 80, 55, 47, 55, 55, 15, 8, 1, 1, 1, 1, 1, 1, 1, 80, 80, 201, 201, 201, 201, 201, 185, 185, 157, 157, 80, 80, 47, 16, 16, 8, 8, 80, 80] 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: 701 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567657 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567657 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567657/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567657 Building REAL300025567658 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567658' /scratch/stefan/7901150/working/building/REAL300025567658 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025567658 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567658/0 /scratch/stefan/7901150/working/building/REAL300025567658 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 163) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/163 `/scratch/stefan/7901150/working/3D/163' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)NC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C(F)=C1) `REAL300025567658.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567658/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567658 none CS(=O)(=O)NC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [5, 14, 11, 11, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 15, 1, 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, 6, 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: [16, 8, 16, 16, 1, 1, 1, 1, 1, 1, 7, 7, 7, 15, 38, 52, 124, 124, 124, 124, 124, 1, 1, 1, 16, 16, 16, 8, 1, 1, 15, 38, 38, 52, 52, 1] 201 rigid atoms, others: [35, 4, 5, 6, 7, 8, 9, 21, 22, 23, 28, 29] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 30, 31, 32, 33, 34]) total number of confs: 404 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567658 none CS(=O)(=O)NC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [5, 14, 11, 11, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 15, 1, 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, 6, 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, 174, 201, 201, 124, 109, 124, 124, 76, 48, 76, 76, 17, 8, 1, 1, 1, 1, 1, 1, 1, 124, 124, 124, 201, 201, 201, 174, 124, 124, 48, 17, 17, 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]) total number of confs: 822 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567658 /scratch/stefan/7901150/working /scratch/stefan/7901150 mkdir: created directory `1' /scratch/stefan/7901150/working/building/REAL300025567658/1 /scratch/stefan/7901150/working/building/REAL300025567658 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 1 (index: 164) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/164 `/scratch/stefan/7901150/working/3D/164' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)[N-]C1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C(F)=C1) `REAL300025567658.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025567658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567658/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567658 none CS(=O)(=O)[N-]C1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 14, 11, 11, 8, 1, 1, 1, 1, 14, 11, 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, 3, 3, 7, 7, 7, 7, 7, 7, 6, 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: [8, 7, 8, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 14, 41, 49, 97, 97, 97, 97, 97, 1, 1, 1, 8, 8, 8, 1, 1, 14, 41, 41, 49, 49, 1] 201 rigid atoms, others: [34, 4, 5, 6, 7, 8, 9, 21, 22, 23, 27, 28] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 29, 30, 31, 32, 33]) total number of confs: 304 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567658 none CS(=O)(=O)[N-]C1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 14, 11, 11, 8, 1, 1, 1, 1, 14, 11, 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, 3, 3, 7, 7, 7, 7, 7, 7, 6, 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, 97, 80, 97, 97, 62, 39, 62, 62, 13, 7, 1, 1, 1, 1, 1, 1, 1, 97, 97, 97, 201, 201, 201, 97, 97, 39, 13, 13, 7, 7, 97] 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: 542 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567658 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567658 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 1: /scratch/stefan/7901150/working/building/REAL300025567658/1.* 0: /scratch/stefan/7901150/working/building/REAL300025567658/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567658 Building REAL300025567659 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567659' /scratch/stefan/7901150/working/building/REAL300025567659 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025567659 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567659/0 /scratch/stefan/7901150/working/building/REAL300025567659 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 165) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/165 `/scratch/stefan/7901150/working/3D/165' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CC[N-]S(=O)(=O)C2=C(F)C=CC=C2[N+](=O)[O-])[N-]O1) `REAL300025567659.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567659.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567659/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567659 none O=C1N=C(CC[N-]S(=O)(=O)C2=C(F)C=CC=C2[N+](=O)[O-])[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 15, 1, 1, 1, 1, 8, 11, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 3, 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: [1, 1, 1, 1, 1, 5, 5, 19, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 5, 5, 5, 5, 23, 23, 23] 23 rigid atoms, others: [0, 1, 2, 3, 4, 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]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567659 none O=C1N=C(CC[N-]S(=O)(=O)C2=C(F)C=CC=C2[N+](=O)[O-])[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 15, 1, 1, 1, 1, 8, 11, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 3, 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, 9, 9, 5, 4, 1, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 23, 23, 9, 9, 9, 9, 1, 1, 1] 23 rigid atoms, others: [7, 10, 11, 12, 13, 14, 15, 16, 17, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 57 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567659 /scratch/stefan/7901150/working /scratch/stefan/7901150 mkdir: created directory `1' /scratch/stefan/7901150/working/building/REAL300025567659/1 /scratch/stefan/7901150/working/building/REAL300025567659 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 1 (index: 166) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/166 `/scratch/stefan/7901150/working/3D/166' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2=C(F)C=CC=C2[N+](=O)[O-])[N-]O1) `REAL300025567659.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025567659.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567659/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567659 none O=C1N=C(CCNS(=O)(=O)C2=C(F)C=CC=C2[N+](=O)[O-])[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 15, 1, 1, 1, 1, 8, 11, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 3, 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: [1, 1, 1, 1, 1, 9, 23, 81, 122, 122, 122, 124, 124, 124, 124, 124, 124, 124, 124, 124, 1, 1, 9, 9, 23, 23, 81, 124, 124, 124] 124 rigid atoms, others: [0, 1, 2, 3, 4, 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]) total number of confs: 462 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567659 none O=C1N=C(CCNS(=O)(=O)C2=C(F)C=CC=C2[N+](=O)[O-])[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 15, 1, 1, 1, 1, 8, 11, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 3, 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: [124, 124, 124, 58, 38, 7, 4, 1, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 124, 124, 58, 58, 38, 38, 7, 1, 1, 1] 124 rigid atoms, others: [7, 10, 11, 12, 13, 14, 15, 16, 17, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 18, 19, 20, 21, 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 /scratch/stefan/7901150/working/building/REAL300025567659 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567659 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 1: /scratch/stefan/7901150/working/building/REAL300025567659/1.* 0: /scratch/stefan/7901150/working/building/REAL300025567659/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567659 Building REAL300025567660 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567660' /scratch/stefan/7901150/working/building/REAL300025567660 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567660 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567660/0 /scratch/stefan/7901150/working/building/REAL300025567660 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 167) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/167 `/scratch/stefan/7901150/working/3D/167' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2=CN(C3=CC=CC=C3)N=C2)[N-]O1) `REAL300025567660.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567660.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567660/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567660 none O=C1N=C(CCNS(=O)(=O)C2=CN(C3=CC=CC=C3)N=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 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 201 conformations in 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, 23, 88, 153, 153, 153, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 9, 9, 23, 23, 88, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 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: 703 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567660 none O=C1N=C(CCNS(=O)(=O)C2=CN(C3=CC=CC=C3)N=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 97, 57, 9, 3, 1, 3, 3, 1, 1, 1, 1, 4, 4, 2, 4, 4, 1, 1, 201, 201, 97, 97, 57, 57, 9, 1, 4, 4, 2, 4, 4, 1] 201 rigid atoms, others: [34, 7, 10, 11, 12, 13, 19, 20, 28] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33]) total number of confs: 608 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567660 none O=C1N=C(CCNS(=O)(=O)C2=CN(C3=CC=CC=C3)N=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 103, 67, 17, 7, 4, 7, 7, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 201, 201, 103, 103, 67, 67, 17, 4, 1, 1, 1, 1, 1, 4] 201 rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 34]) total number of confs: 609 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567660 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567660 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567660/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567660 Building REAL300025567661 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567661' /scratch/stefan/7901150/working/building/REAL300025567661 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567661 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567661/0 /scratch/stefan/7901150/working/building/REAL300025567661 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 168) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/168 `/scratch/stefan/7901150/working/3D/168' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2=CN(CC3=CC=CC=C3)N=C2)[N-]O1) `REAL300025567661.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567661/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567661 none O=C1N=C(CCNS(=O)(=O)C2=CN(CC3=CC=CC=C3)N=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 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, 1, 9, 19, 63, 90, 90, 90, 114, 114, 114, 201, 201, 201, 201, 201, 201, 114, 114, 1, 1, 9, 9, 19, 19, 63, 114, 201, 201, 201, 201, 201, 201, 201, 114] 201 rigid atoms, others: [0, 1, 2, 3, 4, 22, 23] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 798 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567661 none O=C1N=C(CCNS(=O)(=O)C2=CN(CC3=CC=CC=C3)N=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 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: [114, 114, 114, 49, 34, 9, 2, 1, 2, 2, 1, 1, 1, 1, 8, 14, 14, 11, 14, 14, 1, 1, 114, 114, 49, 49, 34, 34, 9, 1, 8, 8, 14, 14, 14, 14, 14, 1] 201 rigid atoms, others: [37, 7, 10, 11, 12, 13, 20, 21, 29] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 370 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567661 none O=C1N=C(CCNS(=O)(=O)C2=CN(CC3=CC=CC=C3)N=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 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: [201, 201, 201, 107, 92, 39, 21, 14, 21, 21, 14, 14, 3, 1, 1, 1, 1, 1, 1, 1, 14, 14, 201, 201, 107, 107, 92, 92, 39, 14, 3, 3, 1, 1, 1, 1, 1, 14] 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, 37]) total number of confs: 612 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567661 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567661 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567661/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567661 Building REAL300025567662 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567662' /scratch/stefan/7901150/working/building/REAL300025567662 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567662 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567662/0 /scratch/stefan/7901150/working/building/REAL300025567662 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 169) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/169 `/scratch/stefan/7901150/working/3D/169' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)CC2=CC=CC(F)=C2)[N-]O1) `REAL300025567662.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567662.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567662/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567662 none O=C1N=C(CCNS(=O)(=O)CC2=CC=CC(F)=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 5, 1, 1, 1, 1, 1, 15, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 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: [1, 1, 1, 1, 1, 8, 22, 68, 93, 93, 93, 118, 201, 201, 201, 201, 201, 201, 1, 1, 8, 8, 22, 22, 68, 118, 118, 201, 201, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 18, 19] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 653 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567662 none O=C1N=C(CCNS(=O)(=O)CC2=CC=CC(F)=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 5, 1, 1, 1, 1, 1, 15, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 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: [201, 201, 201, 124, 104, 41, 14, 6, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 124, 124, 104, 104, 41, 6, 6, 1, 1, 1, 1] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 671 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567662 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567662 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567662/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567662 Building REAL300025567663 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567663' /scratch/stefan/7901150/working/building/REAL300025567663 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567663 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567663/0 /scratch/stefan/7901150/working/building/REAL300025567663 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 170) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/170 `/scratch/stefan/7901150/working/3D/170' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2=CC=C(OCC3=CC=CC=C3)C=C2)[N-]O1) `REAL300025567663.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567663.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567663/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567663 none O=C1N=C(CCNS(=O)(=O)C2=CC=C(OCC3=CC=CC=C3)C=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', '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, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 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] 0 hydrogens need rotated 201 conformations in 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, 21, 73, 120, 120, 120, 120, 120, 120, 120, 201, 201, 201, 201, 201, 201, 201, 120, 120, 1, 1, 9, 9, 21, 21, 73, 120, 120, 201, 201, 201, 201, 201, 201, 201, 120, 120] 201 rigid atoms, others: [0, 1, 2, 3, 4, 24, 25] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 633 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567663 none O=C1N=C(CCNS(=O)(=O)C2=CC=C(OCC3=CC=CC=C3)C=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', '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, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 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] 0 hydrogens 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, 37, 21, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 2, 2, 6, 6, 2, 6, 6, 1, 1, 120, 120, 37, 37, 21, 21, 5, 1, 1, 2, 2, 6, 6, 2, 6, 6, 1, 1] 201 rigid atoms, others: [32, 7, 40, 41, 10, 11, 12, 13, 14, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 290 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567663 none O=C1N=C(CCNS(=O)(=O)C2=CC=C(OCC3=CC=CC=C3)C=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', '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, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 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] 0 hydrogens need rotated 201 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, 76, 23, 7, 6, 7, 7, 6, 6, 6, 3, 3, 1, 1, 1, 1, 1, 1, 1, 6, 6, 201, 201, 105, 105, 76, 76, 23, 6, 6, 3, 3, 1, 1, 1, 1, 1, 6, 6] 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, 40, 41]) total number of confs: 626 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567663 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567663 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567663/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567663 Building REAL300025567664 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567664' /scratch/stefan/7901150/working/building/REAL300025567664 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567664 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567664/0 /scratch/stefan/7901150/working/building/REAL300025567664 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 171) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/171 `/scratch/stefan/7901150/working/3D/171' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(Cl)C=C1CS(=O)(=O)NCCC1=NC(=O)O[N-]1) `REAL300025567664.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567664/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567664 none COC1=CC=C(Cl)C=C1CS(=O)(=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', 'Cl', 'C.ar', 'C.ar', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.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, 1, 16, 1, 1, 5, 14, 11, 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, 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, 1, 1, 1, 1, 1, 1, 1, 1, 4, 14, 14, 14, 38, 82, 96, 200, 200, 200, 200, 200, 4, 4, 4, 1, 1, 1, 4, 4, 38, 82, 82, 96, 96] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 25, 26, 27] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 591 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567664 none COC1=CC=C(Cl)C=C1CS(=O)(=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', 'Cl', 'C.ar', 'C.ar', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.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, 1, 16, 1, 1, 5, 14, 11, 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, 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, 200, 200, 200, 182, 200, 200, 200, 122, 81, 56, 81, 81, 19, 7, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 200, 200, 200, 122, 122, 56, 20, 20, 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]) total number of confs: 791 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567664 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567664 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567664/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567664 Building REAL300025567665 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567665' /scratch/stefan/7901150/working/building/REAL300025567665 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567665 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567665/0 /scratch/stefan/7901150/working/building/REAL300025567665 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 172) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/172 `/scratch/stefan/7901150/working/3D/172' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)CC2=CC=C(OC(F)(F)F)C=C2)[N-]O1) `REAL300025567665.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567665.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567665/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567665 none O=C1N=C(CCNS(=O)(=O)CC2=CC=C(OC(F)(F)F)C=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 5, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 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] 0 hydrogens need rotated 201 conformations in 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, 18, 37, 47, 47, 47, 81, 85, 85, 83, 85, 201, 201, 201, 201, 85, 85, 1, 1, 8, 8, 18, 18, 37, 81, 81, 85, 85, 85, 85] 201 rigid atoms, others: [0, 1, 2, 3, 4, 22, 23] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 552 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567665 none O=C1N=C(CCNS(=O)(=O)CC2=CC=C(OC(F)(F)F)C=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 5, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [85, 85, 85, 31, 31, 17, 5, 3, 5, 5, 1, 1, 1, 1, 1, 1, 12, 16, 16, 16, 1, 1, 85, 85, 31, 31, 31, 31, 17, 3, 3, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 243 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567665 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567665 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567665/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567665 Building REAL300025567666 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567666' /scratch/stefan/7901150/working/building/REAL300025567666 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567666 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567666/0 /scratch/stefan/7901150/working/building/REAL300025567666 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 173) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/173 `/scratch/stefan/7901150/working/3D/173' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2CCS(=O)(=O)CC2)[N-]O1) `REAL300025567666.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567666.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567666/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567666 none O=C1N=C(CCNS(=O)(=O)C2CCS(=O)(=O)CC2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 5, 5, 5, 14, 11, 11, 5, 5, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 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, 1, 9, 24, 77, 120, 120, 120, 127, 127, 127, 127, 127, 127, 127, 1, 1, 9, 9, 24, 24, 77, 127, 127, 127, 127, 127, 127, 127, 127, 127] 127 rigid atoms, others: [0, 1, 2, 3, 4, 18, 19] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 495 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567666 none O=C1N=C(CCNS(=O)(=O)C2CCS(=O)(=O)CC2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 5, 5, 5, 14, 11, 11, 5, 5, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 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, 127, 75, 65, 22, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 127, 127, 75, 75, 65, 65, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1] 127 rigid atoms, others: [32, 33, 7, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 399 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567666 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567666 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567666/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567666 Building REAL300025567667 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567667' /scratch/stefan/7901150/working/building/REAL300025567667 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567667 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567667/0 /scratch/stefan/7901150/working/building/REAL300025567667 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 174) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/174 `/scratch/stefan/7901150/working/3D/174' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2=CC(Br)=CC=C2F)[N-]O1) `REAL300025567667.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567667.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567667/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567667 none O=C1N=C(CCNS(=O)(=O)C2=CC(Br)=CC=C2F)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 17, 1, 1, 1, 15, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 9, 24, 79, 137, 137, 137, 201, 201, 201, 193, 201, 201, 201, 1, 1, 9, 9, 24, 24, 79, 201, 198, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 18, 19] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 700 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567667 none O=C1N=C(CCNS(=O)(=O)C2=CC(Br)=CC=C2F)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 17, 1, 1, 1, 15, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 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: [201, 201, 201, 102, 76, 25, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 102, 102, 76, 76, 25, 1, 1, 1] 201 rigid atoms, others: [7, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 606 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567667 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567667 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567667/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567667 Building REAL300025567668 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567668' /scratch/stefan/7901150/working/building/REAL300025567668 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567668 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567668/0 /scratch/stefan/7901150/working/building/REAL300025567668 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 175) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/175 `/scratch/stefan/7901150/working/3D/175' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1C(F)(F)F) `REAL300025567668.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567668.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567668/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567668 none CC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1C(F)(F)F 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.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'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 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, 2, 2, 2, 9, 57, 90, 201, 201, 201, 201, 201, 1, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1, 9, 57, 57, 90, 90, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 33, 17, 18, 19, 26, 27] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 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 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567668 none CC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1C(F)(F)F 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.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'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 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, 118, 76, 118, 118, 24, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 76, 25, 25, 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]) total number of confs: 647 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567668 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567668 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567668/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567668 Building REAL300025567669 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567669' /scratch/stefan/7901150/working/building/REAL300025567669 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567669 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567669/0 /scratch/stefan/7901150/working/building/REAL300025567669 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 176) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/176 `/scratch/stefan/7901150/working/3D/176' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CSC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=C1) `REAL300025567669.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567669.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567669/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567669 none COC(=O)C1=CSC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 14, 1, 14, 11, 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, 5, 7, 7, 7, 7, 7, 6, 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: [4, 4, 1, 4, 1, 1, 1, 1, 1, 6, 6, 6, 25, 63, 83, 157, 157, 157, 157, 157, 1, 5, 5, 5, 1, 25, 63, 63, 83, 83, 1] 201 rigid atoms, others: [2, 4, 5, 6, 7, 8, 20, 24, 30] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 25, 26, 27, 28, 29]) total number of confs: 507 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567669 none COC(=O)C1=CSC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 14, 1, 14, 11, 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, 5, 7, 7, 7, 7, 7, 6, 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, 157, 201, 157, 157, 157, 93, 56, 93, 93, 19, 7, 1, 1, 1, 1, 1, 1, 1, 157, 201, 201, 201, 157, 56, 19, 19, 7, 7, 157] 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: 657 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567669 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567669 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567669/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567669 Building REAL300025567670 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567670' /scratch/stefan/7901150/working/building/REAL300025567670 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567670 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567670/0 /scratch/stefan/7901150/working/building/REAL300025567670 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 177) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/177 `/scratch/stefan/7901150/working/3D/177' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC=C([N+](=O)[O-])C=C1S(=O)(=O)NCCC1=NC(=O)O[N-]1) `REAL300025567670.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567670.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567670/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567670 none CCC1=CC=C([N+](=O)[O-])C=C1S(=O)(=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', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.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, 5, 1, 1, 1, 1, 8, 11, 11, 1, 1, 14, 11, 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, 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: [6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 9, 39, 65, 191, 191, 191, 191, 191, 6, 6, 6, 5, 5, 1, 1, 1, 9, 39, 39, 65, 65] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 28, 29, 30] set([0, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35]) total number of confs: 489 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567670 none CCC1=CC=C([N+](=O)[O-])C=C1S(=O)(=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', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.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, 5, 1, 1, 1, 1, 8, 11, 11, 1, 1, 14, 11, 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, 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, 191, 191, 191, 167, 191, 191, 191, 191, 191, 167, 102, 167, 167, 25, 9, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 191, 167, 191, 102, 25, 25, 9, 9] 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: 836 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567670 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567670 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567670/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567670 Building REAL300025567671 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567671' /scratch/stefan/7901150/working/building/REAL300025567671 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567671 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567671/0 /scratch/stefan/7901150/working/building/REAL300025567671 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 178) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/178 `/scratch/stefan/7901150/working/3D/178' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C(=O)N(C)C2=CC(S(=O)(=O)NCCC3=NC(=O)O[N-]3)=CC=C21) `REAL300025567671.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567671.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567671/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567671 none CN1C(=O)N(C)C2=CC(S(=O)(=O)NCCC3=NC(=O)O[N-]3)=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 8, 1, 11, 8, 5, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 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, 6, 6, 4, 7, 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, 1, 1, 1, 1, 2, 2, 2, 9, 57, 93, 201, 201, 201, 201, 201, 1, 1, 1, 2, 2, 2, 2, 2, 2, 1, 9, 57, 57, 93, 93, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 21, 22, 23, 36, 30, 37] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 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 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567671 none CN1C(=O)N(C)C2=CC(S(=O)(=O)NCCC3=NC(=O)O[N-]3)=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 8, 1, 11, 8, 5, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 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, 6, 6, 4, 7, 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, 201, 201, 113, 82, 113, 113, 24, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 82, 24, 24, 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]) total number of confs: 603 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567671 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567671 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567671/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567671 Building REAL300025567672 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567672' /scratch/stefan/7901150/working/building/REAL300025567672 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567672 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567672/0 /scratch/stefan/7901150/working/building/REAL300025567672 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 179) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/179 `/scratch/stefan/7901150/working/3D/179' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2=CC3=CC=C(OC(F)F)C=C3CC2)[N-]O1) `REAL300025567672.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567672.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567672/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567672 none O=C1N=C(CCNS(=O)(=O)C2=CC3=CC=C(OC(F)F)C=C3CC2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 5, 5, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 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] 0 hydrogens need rotated 201 conformations in 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, 15, 33, 42, 42, 42, 81, 81, 81, 81, 81, 81, 200, 201, 201, 81, 81, 81, 81, 1, 1, 7, 7, 15, 15, 33, 81, 81, 81, 201, 81, 81, 81, 81, 81] 201 rigid atoms, others: [0, 1, 2, 3, 4, 24, 25] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 425 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567672 none O=C1N=C(CCNS(=O)(=O)C2=CC3=CC=C(OC(F)F)C=C3CC2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 5, 5, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [81, 81, 81, 38, 37, 21, 13, 1, 13, 13, 1, 1, 1, 1, 1, 1, 1, 11, 22, 22, 1, 1, 1, 1, 81, 81, 38, 38, 37, 37, 21, 1, 1, 1, 22, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 35, 36, 37, 38, 7, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 39, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 34, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 292 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567672 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567672 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567672/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567672 Building REAL300025567673 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567673' /scratch/stefan/7901150/working/building/REAL300025567673 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567673 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567673/0 /scratch/stefan/7901150/working/building/REAL300025567673 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 180) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/180 `/scratch/stefan/7901150/working/3D/180' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2=CC=CC3=NC=CC=C23)[N-]O1) `REAL300025567673.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567673.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567673/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567673 none O=C1N=C(CCNS(=O)(=O)C2=CC=CC3=NC=CC=C23)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 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: [1, 1, 1, 1, 1, 9, 25, 73, 129, 129, 129, 129, 129, 129, 129, 129, 129, 129, 129, 129, 1, 1, 9, 9, 25, 25, 73, 129, 129, 129, 129, 129, 129] 129 rigid atoms, others: [0, 1, 2, 3, 4, 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, 32]) total number of confs: 546 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567673 none O=C1N=C(CCNS(=O)(=O)C2=CC=CC3=NC=CC=C23)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 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: [129, 129, 129, 51, 29, 7, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 129, 129, 51, 51, 29, 29, 7, 1, 1, 1, 1, 1, 1] 129 rigid atoms, others: [32, 7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 350 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567673 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567673 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567673/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567673 Building REAL300025567674 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567674' /scratch/stefan/7901150/working/building/REAL300025567674 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567674 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567674/0 /scratch/stefan/7901150/working/building/REAL300025567674 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 181) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/181 `/scratch/stefan/7901150/working/3D/181' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2=CSC(C3=CC=C(F)C=C3)=N2)[N-]O1) `REAL300025567674.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567674.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567674/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567674 none O=C1N=C(CCNS(=O)(=O)C2=CSC(C3=CC=C(F)C=C3)=N2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 14, 1, 1, 1, 1, 1, 15, 1, 1, 8, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 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 201 conformations in 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, 23, 72, 111, 111, 111, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 9, 9, 23, 23, 72, 201, 201, 201, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 22, 23] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 599 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567674 none O=C1N=C(CCNS(=O)(=O)C2=CSC(C3=CC=C(F)C=C3)=N2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 14, 1, 1, 1, 1, 1, 15, 1, 1, 8, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 95, 71, 25, 6, 1, 6, 6, 1, 1, 1, 1, 1, 4, 4, 2, 2, 4, 4, 1, 201, 201, 95, 95, 71, 71, 25, 1, 4, 4, 4, 4] 201 rigid atoms, others: [7, 10, 11, 12, 13, 14, 21, 29] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33]) 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567674 none O=C1N=C(CCNS(=O)(=O)C2=CSC(C3=CC=C(F)C=C3)=N2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 14, 1, 1, 1, 1, 1, 15, 1, 1, 8, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 120, 114, 59, 19, 4, 19, 19, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 201, 201, 120, 120, 114, 114, 59, 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: 627 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567674 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567674 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567674/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567674 Building REAL300025567675 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567675' /scratch/stefan/7901150/working/building/REAL300025567675 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567675 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567675/0 /scratch/stefan/7901150/working/building/REAL300025567675 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 182) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/182 `/scratch/stefan/7901150/working/3D/182' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2=CC=C(Cl)N=C2Cl)[N-]O1) `REAL300025567675.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567675.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567675/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567675 none O=C1N=C(CCNS(=O)(=O)C2=CC=C(Cl)N=C2Cl)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'Cl', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 16, 8, 1, 16, 8, 12, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 191 conformations in input total number of sets (complete confs): 191 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 9, 25, 104, 171, 171, 171, 191, 191, 191, 191, 191, 191, 191, 1, 1, 9, 9, 25, 25, 104, 191, 191] 191 rigid atoms, others: [0, 1, 2, 3, 4, 18, 19] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 690 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567675 none O=C1N=C(CCNS(=O)(=O)C2=CC=C(Cl)N=C2Cl)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'Cl', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 16, 8, 1, 16, 8, 12, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 191 conformations in input total number of sets (complete confs): 191 using faster count positions algorithm for large data unique positions, atoms: [191, 191, 191, 89, 57, 17, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 191, 191, 89, 89, 57, 57, 17, 1, 1] 191 rigid atoms, others: [7, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 546 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567675 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567675 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567675/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567675 Building REAL300025567676 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567676' /scratch/stefan/7901150/working/building/REAL300025567676 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567676 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567676/0 /scratch/stefan/7901150/working/building/REAL300025567676 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 183) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/183 `/scratch/stefan/7901150/working/3D/183' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NOC2=NC=C(S(=O)(=O)NCCC3=NC(=O)O[N-]3)C=C12) `REAL300025567676.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567676.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567676/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567676 none CC1=NOC2=NC=C(S(=O)(=O)NCCC3=NC(=O)O[N-]3)C=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [5, 1, 8, 12, 1, 8, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 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, 1, 1, 2, 2, 2, 9, 54, 86, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 1, 9, 54, 54, 86, 86, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 25, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 26, 27, 28, 29, 30]) total number of confs: 550 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567676 none CC1=NOC2=NC=C(S(=O)(=O)NCCC3=NC(=O)O[N-]3)C=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [5, 1, 8, 12, 1, 8, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 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, 145, 88, 145, 145, 24, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 88, 24, 24, 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]) total number of confs: 695 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567676 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567676 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567676/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567676 Building REAL300025567677 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567677' /scratch/stefan/7901150/working/building/REAL300025567677 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025567677 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567677/0 /scratch/stefan/7901150/working/building/REAL300025567677 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 184) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/184 `/scratch/stefan/7901150/working/3D/184' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(F)=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C(F)=C1) `REAL300025567677.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567677.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567677/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567677 none COC1=CC(F)=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 15, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 15, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 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, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 22, 64, 89, 201, 201, 201, 201, 201, 1, 1, 1, 2, 2, 2, 1, 22, 64, 64, 89, 89, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 25, 31] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 26, 27, 28, 29, 30]) total number of confs: 564 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567677 none COC1=CC(F)=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 15, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 15, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 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, 154, 133, 201, 201, 201, 133, 77, 133, 133, 18, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 77, 19, 19, 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: 958 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567677 /scratch/stefan/7901150/working /scratch/stefan/7901150 mkdir: created directory `1' /scratch/stefan/7901150/working/building/REAL300025567677/1 /scratch/stefan/7901150/working/building/REAL300025567677 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 1 (index: 185) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/185 `/scratch/stefan/7901150/working/3D/185' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(F)=C(S(=O)(=O)[N-]CCC2=NC(=O)O[N-]2)C(F)=C1) `REAL300025567677.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025567677.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567677/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567677 none COC1=CC(F)=C(S(=O)(=O)[N-]CCC2=NC(=O)O[N-]2)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 15, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 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, 1, 13, 13, 13, 35, 91, 91, 201, 201, 201, 201, 201, 1, 1, 1, 2, 2, 2, 1, 91, 91, 91, 91, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 25, 30] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 26, 27, 28, 29]) total number of confs: 493 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567677 none COC1=CC(F)=C(S(=O)(=O)[N-]CCC2=NC(=O)O[N-]2)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 15, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 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, 187, 126, 201, 201, 201, 126, 41, 126, 126, 8, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 8, 8, 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]) total number of confs: 910 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567677 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567677 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 1: /scratch/stefan/7901150/working/building/REAL300025567677/1.* 0: /scratch/stefan/7901150/working/building/REAL300025567677/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567677 Building REAL300025567678 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567678' /scratch/stefan/7901150/working/building/REAL300025567678 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567678 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567678/0 /scratch/stefan/7901150/working/building/REAL300025567678 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 186) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/186 `/scratch/stefan/7901150/working/3D/186' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)CC2=CC=CC(C(F)(F)F)=C2)[N-]O1) `REAL300025567678.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567678.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567678/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567678 none O=C1N=C(CCNS(=O)(=O)CC2=CC=CC(C(F)(F)F)=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 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: [1, 1, 1, 1, 1, 8, 19, 66, 98, 98, 98, 135, 201, 201, 197, 201, 201, 201, 201, 201, 201, 1, 1, 8, 8, 19, 19, 66, 135, 135, 201, 201, 199, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 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]) total number of confs: 727 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567678 none O=C1N=C(CCNS(=O)(=O)CC2=CC=CC(C(F)(F)F)=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 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: [201, 201, 201, 112, 96, 45, 16, 6, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 112, 112, 96, 96, 45, 6, 6, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 630 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567678 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567678 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567678/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567678 Building REAL300025567679 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567679' /scratch/stefan/7901150/working/building/REAL300025567679 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567679 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567679/0 /scratch/stefan/7901150/working/building/REAL300025567679 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 187) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/187 `/scratch/stefan/7901150/working/3D/187' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2=CC=C(CCCCl)C=C2)[N-]O1) `REAL300025567679.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567679.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567679/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567679 none O=C1N=C(CCNS(=O)(=O)C2=CC=C(CCCCl)C=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'Cl', '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: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 5, 5, 5, 16, 1, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 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, 1, 1, 8, 14, 34, 48, 48, 48, 48, 48, 48, 48, 89, 93, 201, 48, 48, 1, 1, 8, 8, 14, 14, 34, 48, 48, 89, 89, 93, 93, 201, 201, 48, 48] 201 rigid atoms, others: [0, 1, 2, 3, 4, 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, 32, 33, 34, 35, 36]) total number of confs: 972 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567679 none O=C1N=C(CCNS(=O)(=O)C2=CC=C(CCCCl)C=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'Cl', '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: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 5, 5, 5, 16, 1, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 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: [48, 48, 48, 25, 15, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 4, 8, 1, 1, 48, 48, 25, 25, 15, 15, 5, 1, 1, 2, 2, 4, 4, 8, 8, 1, 1] 201 rigid atoms, others: [35, 36, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 27, 28] set([0, 1, 2, 3, 4, 5, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34]) total number of confs: 186 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567679 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567679 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567679/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567679 Building REAL300025567680 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567680' /scratch/stefan/7901150/working/building/REAL300025567680 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567680 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567680/0 /scratch/stefan/7901150/working/building/REAL300025567680 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 188) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/188 `/scratch/stefan/7901150/working/3D/188' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)CC2=CC=C(Br)C=C2F)[N-]O1) `REAL300025567680.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567680.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567680/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567680 none O=C1N=C(CCNS(=O)(=O)CC2=CC=C(Br)C=C2F)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 5, 1, 1, 1, 1, 17, 1, 1, 15, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 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: [1, 1, 1, 1, 1, 8, 22, 75, 113, 113, 113, 149, 201, 201, 201, 201, 201, 201, 201, 1, 1, 8, 8, 22, 22, 75, 149, 149, 201, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 19, 20] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 738 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567680 none O=C1N=C(CCNS(=O)(=O)CC2=CC=C(Br)C=C2F)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 5, 1, 1, 1, 1, 17, 1, 1, 15, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 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: [201, 201, 201, 131, 107, 37, 12, 4, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 131, 131, 107, 107, 37, 4, 4, 1, 1, 1] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 693 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567680 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567680 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567680/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567680 Building REAL300025567681 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567681' /scratch/stefan/7901150/working/building/REAL300025567681 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567681 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567681/0 /scratch/stefan/7901150/working/building/REAL300025567681 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 189) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/189 `/scratch/stefan/7901150/working/3D/189' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)CC2=CC=CC=C2Cl)[N-]O1) `REAL300025567681.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567681.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567681/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567681 none O=C1N=C(CCNS(=O)(=O)CC2=CC=CC=C2Cl)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 1, 5, 5, 8, 14, 11, 11, 5, 1, 1, 1, 1, 1, 1, 16, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 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: [1, 1, 1, 1, 1, 9, 23, 78, 117, 117, 117, 146, 201, 201, 201, 201, 201, 201, 1, 1, 9, 9, 23, 23, 78, 146, 146, 201, 201, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 18, 19] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 724 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567681 none O=C1N=C(CCNS(=O)(=O)CC2=CC=CC=C2Cl)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 1, 5, 5, 8, 14, 11, 11, 5, 1, 1, 1, 1, 1, 1, 16, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 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: [201, 201, 201, 123, 99, 32, 11, 3, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 123, 123, 99, 99, 32, 3, 3, 1, 1, 1, 1] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 680 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567681 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567681 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567681/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567681 Building REAL300025567682 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567682' /scratch/stefan/7901150/working/building/REAL300025567682 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567682 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567682/0 /scratch/stefan/7901150/working/building/REAL300025567682 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 190) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/190 `/scratch/stefan/7901150/working/3D/190' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2=CC=C(N3CCCS3(=O)=O)C=C2)[N-]O1) `REAL300025567682.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567682.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567682/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567682 none O=C1N=C(CCNS(=O)(=O)C2=CC=C(N3CCCS3(=O)=O)C=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 5, 5, 5, 14, 11, 11, 1, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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, 9, 22, 75, 115, 115, 115, 115, 115, 115, 115, 201, 201, 201, 201, 201, 201, 115, 115, 1, 1, 9, 9, 22, 22, 75, 115, 115, 201, 201, 201, 201, 201, 201, 115, 115] 201 rigid atoms, others: [0, 1, 2, 3, 4, 23, 24] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 587 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567682 none O=C1N=C(CCNS(=O)(=O)C2=CC=C(N3CCCS3(=O)=O)C=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 5, 5, 5, 14, 11, 11, 1, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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: [115, 115, 115, 40, 25, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 1, 1, 115, 115, 40, 40, 25, 25, 5, 1, 1, 12, 12, 12, 12, 12, 12, 1, 1] 201 rigid atoms, others: [38, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 39, 30, 31] set([0, 1, 2, 3, 4, 5, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37]) total number of confs: 284 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567682 none O=C1N=C(CCNS(=O)(=O)C2=CC=C(N3CCCS3(=O)=O)C=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 5, 5, 5, 14, 11, 11, 1, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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, 123, 93, 31, 12, 2, 12, 12, 1, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 201, 201, 123, 123, 93, 93, 31, 12, 12, 1, 1, 1, 1, 1, 1, 12, 12] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39]) total number of confs: 707 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567682 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567682 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567682/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567682 Building REAL300025567683 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567683' /scratch/stefan/7901150/working/building/REAL300025567683 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025567683 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567683/0 /scratch/stefan/7901150/working/building/REAL300025567683 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 191) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/191 `/scratch/stefan/7901150/working/3D/191' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2=CC=CC(F)=C2F)[N-]O1) `REAL300025567683.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567683/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567683 none O=C1N=C(CCNS(=O)(=O)C2=CC=CC(F)=C2F)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 15, 1, 15, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 9, 22, 78, 131, 131, 131, 201, 201, 201, 201, 201, 201, 201, 1, 1, 9, 9, 22, 22, 78, 201, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 18, 19] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 616 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567683 none O=C1N=C(CCNS(=O)(=O)C2=CC=CC(F)=C2F)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 15, 1, 15, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 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: [201, 201, 201, 99, 74, 25, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 99, 99, 74, 74, 25, 1, 1, 1] 201 rigid atoms, others: [7, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 593 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567683 /scratch/stefan/7901150/working /scratch/stefan/7901150 mkdir: created directory `1' /scratch/stefan/7901150/working/building/REAL300025567683/1 /scratch/stefan/7901150/working/building/REAL300025567683 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 1 (index: 192) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/192 `/scratch/stefan/7901150/working/3D/192' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CC[N-]S(=O)(=O)C2=CC=CC(F)=C2F)[N-]O1) `REAL300025567683.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025567683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567683/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567683 none O=C1N=C(CC[N-]S(=O)(=O)C2=CC=CC(F)=C2F)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 15, 1, 15, 8, 12, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [1, 1, 1, 1, 1, 9, 13, 43, 95, 95, 95, 119, 119, 119, 119, 119, 119, 119, 1, 1, 9, 9, 13, 13, 119, 119, 119] 119 rigid atoms, others: [0, 1, 2, 3, 4, 18, 19] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 378 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567683 none O=C1N=C(CC[N-]S(=O)(=O)C2=CC=CC(F)=C2F)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 15, 1, 15, 8, 12, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 66, 64, 25, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 119, 119, 66, 66, 64, 64, 1, 1, 1] 119 rigid atoms, others: [7, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 18, 19, 20, 21, 22, 23]) total number of confs: 322 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567683 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567683 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 1: /scratch/stefan/7901150/working/building/REAL300025567683/1.* 0: /scratch/stefan/7901150/working/building/REAL300025567683/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567683 Building REAL300025567684 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567684' /scratch/stefan/7901150/working/building/REAL300025567684 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567684 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567684/0 /scratch/stefan/7901150/working/building/REAL300025567684 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 193) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/193 `/scratch/stefan/7901150/working/3D/193' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)CC2=CC=CC=C2F)[N-]O1) `REAL300025567684.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567684/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567684 none O=C1N=C(CCNS(=O)(=O)CC2=CC=CC=C2F)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', '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, 1, 5, 5, 8, 14, 11, 11, 5, 1, 1, 1, 1, 1, 1, 15, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 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: [1, 1, 1, 1, 1, 9, 23, 78, 119, 119, 119, 149, 201, 201, 201, 201, 201, 201, 1, 1, 9, 9, 23, 23, 78, 149, 149, 201, 201, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 18, 19] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 736 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567684 none O=C1N=C(CCNS(=O)(=O)CC2=CC=CC=C2F)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', '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, 1, 5, 5, 8, 14, 11, 11, 5, 1, 1, 1, 1, 1, 1, 15, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 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: [201, 201, 201, 132, 105, 35, 13, 5, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 132, 132, 105, 105, 35, 5, 5, 1, 1, 1, 1] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 696 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567684 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567684 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567684/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567684 Building REAL300025567685 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567685' /scratch/stefan/7901150/working/building/REAL300025567685 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567685 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567685/0 /scratch/stefan/7901150/working/building/REAL300025567685 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 194) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/194 `/scratch/stefan/7901150/working/3D/194' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C(Cl)C=C1S(=O)(=O)NCCC1=NC(=O)O[N-]1) `REAL300025567685.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567685.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567685/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567685 none COC(=O)C1=CC=C(Cl)C=C1S(=O)(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.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, 11, 1, 1, 1, 1, 16, 1, 1, 14, 11, 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, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 9, 41, 63, 139, 139, 139, 139, 139, 7, 7, 7, 1, 1, 1, 9, 41, 41, 63, 63] 201 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 11, 26, 27, 28] set([0, 1, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33]) total number of confs: 420 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567685 none COC(=O)C1=CC=C(Cl)C=C1S(=O)(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.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, 11, 1, 1, 1, 1, 16, 1, 1, 14, 11, 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, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 139, 201, 139, 139, 115, 139, 139, 139, 115, 75, 115, 115, 22, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 139, 139, 139, 75, 22, 22, 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: 871 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567685 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567685 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567685/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567685 Building REAL300025567686 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567686' /scratch/stefan/7901150/working/building/REAL300025567686 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567686 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567686/0 /scratch/stefan/7901150/working/building/REAL300025567686 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 195) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/195 `/scratch/stefan/7901150/working/3D/195' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)CC2=CC=C(Cl)N=C2)[N-]O1) `REAL300025567686.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567686.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567686/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567686 none O=C1N=C(CCNS(=O)(=O)CC2=CC=C(Cl)N=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 5, 1, 1, 1, 1, 16, 8, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 8, 22, 67, 81, 81, 81, 127, 201, 201, 201, 201, 201, 201, 1, 1, 8, 8, 22, 22, 67, 127, 127, 201, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 18, 19] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 664 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567686 none O=C1N=C(CCNS(=O)(=O)CC2=CC=C(Cl)N=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 5, 1, 1, 1, 1, 16, 8, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 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, 201, 201, 123, 109, 47, 16, 6, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 123, 123, 109, 109, 47, 6, 6, 1, 1, 1] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 663 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567686 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567686 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567686/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567686 Building REAL300025567687 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567687' /scratch/stefan/7901150/working/building/REAL300025567687 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025567687 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567687/0 /scratch/stefan/7901150/working/building/REAL300025567687 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 196) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/196 `/scratch/stefan/7901150/working/3D/196' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2=CC(Cl)=CC=C2[N+](=O)[O-])[N-]O1) `REAL300025567687.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567687.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567687/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567687 none O=C1N=C(CCNS(=O)(=O)C2=CC(Cl)=CC=C2[N+](=O)[O-])[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 16, 1, 1, 1, 8, 11, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 91 conformations in input total number of sets (complete confs): 91 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 9, 23, 78, 91, 91, 91, 91, 91, 91, 91, 91, 91, 91, 91, 91, 1, 1, 9, 9, 23, 23, 78, 91, 91, 91] 91 rigid atoms, others: [0, 1, 2, 3, 4, 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]) total number of confs: 318 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567687 none O=C1N=C(CCNS(=O)(=O)C2=CC(Cl)=CC=C2[N+](=O)[O-])[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 16, 1, 1, 1, 8, 11, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 91 conformations in input total number of sets (complete confs): 91 using faster count positions algorithm for large data unique positions, atoms: [91, 91, 91, 45, 29, 5, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 91, 91, 45, 45, 29, 29, 5, 1, 1, 1] 91 rigid atoms, others: [7, 10, 11, 12, 13, 14, 15, 16, 17, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 276 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567687 /scratch/stefan/7901150/working /scratch/stefan/7901150 mkdir: created directory `1' /scratch/stefan/7901150/working/building/REAL300025567687/1 /scratch/stefan/7901150/working/building/REAL300025567687 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 1 (index: 197) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/197 `/scratch/stefan/7901150/working/3D/197' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CC[N-]S(=O)(=O)C2=CC(Cl)=CC=C2[N+](=O)[O-])[N-]O1) `REAL300025567687.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025567687.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567687/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567687 none O=C1N=C(CC[N-]S(=O)(=O)C2=CC(Cl)=CC=C2[N+](=O)[O-])[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 16, 1, 1, 1, 8, 11, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 3, 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: [1, 1, 1, 1, 1, 9, 15, 34, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 1, 1, 9, 9, 15, 15, 53, 53, 53] 53 rigid atoms, others: [0, 1, 2, 3, 4, 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]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567687 none O=C1N=C(CC[N-]S(=O)(=O)C2=CC(Cl)=CC=C2[N+](=O)[O-])[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 16, 1, 1, 1, 8, 11, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 53, 26, 21, 5, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 53, 53, 26, 26, 21, 21, 1, 1, 1] 53 rigid atoms, others: [7, 10, 11, 12, 13, 14, 15, 16, 17, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 152 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567687 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567687 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 1: /scratch/stefan/7901150/working/building/REAL300025567687/1.* 0: /scratch/stefan/7901150/working/building/REAL300025567687/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567687 Building REAL300025567688 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567688' /scratch/stefan/7901150/working/building/REAL300025567688 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567688 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567688/0 /scratch/stefan/7901150/working/building/REAL300025567688 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 198) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/198 `/scratch/stefan/7901150/working/3D/198' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)CC2=CC=CC=C2F)[N-]O1) `REAL300025567688.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567688.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567688/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567688 none O=C1N=C(CCNS(=O)(=O)CC2=CC=CC=C2F)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', '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, 1, 5, 5, 8, 14, 11, 11, 5, 1, 1, 1, 1, 1, 1, 15, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 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: [1, 1, 1, 1, 1, 9, 23, 78, 119, 119, 119, 149, 201, 201, 201, 201, 201, 201, 1, 1, 9, 9, 23, 23, 78, 149, 149, 201, 201, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 18, 19] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 736 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567688 none O=C1N=C(CCNS(=O)(=O)CC2=CC=CC=C2F)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', '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, 1, 5, 5, 8, 14, 11, 11, 5, 1, 1, 1, 1, 1, 1, 15, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 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: [201, 201, 201, 132, 105, 35, 13, 5, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 132, 132, 105, 105, 35, 5, 5, 1, 1, 1, 1] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 696 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567688 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567688 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567688/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567688 Building REAL300025567689 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567689' /scratch/stefan/7901150/working/building/REAL300025567689 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567689 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567689/0 /scratch/stefan/7901150/working/building/REAL300025567689 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 199) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/199 `/scratch/stefan/7901150/working/3D/199' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)CC2=CC=CC=C2C(F)(F)F)[N-]O1) `REAL300025567689.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567689.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567689/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567689 none O=C1N=C(CCNS(=O)(=O)CC2=CC=CC=C2C(F)(F)F)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 5, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 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: [1, 1, 1, 1, 1, 9, 22, 73, 128, 128, 128, 153, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 9, 9, 22, 22, 73, 153, 153, 201, 201, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 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]) total number of confs: 738 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567689 none O=C1N=C(CCNS(=O)(=O)CC2=CC=CC=C2C(F)(F)F)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 5, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 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: [201, 201, 201, 111, 81, 25, 11, 3, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 201, 201, 111, 111, 81, 81, 25, 3, 3, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 16, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 660 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567689 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567689 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567689/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567689 Building REAL300025567690 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567690' /scratch/stefan/7901150/working/building/REAL300025567690 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567690 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567690/0 /scratch/stefan/7901150/working/building/REAL300025567690 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 200) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/200 `/scratch/stefan/7901150/working/3D/200' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C(C)=C1) `REAL300025567690.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567690.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567690/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567690 none CCOC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', '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, 5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 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, 7, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 21, 31, 133, 133, 133, 133, 133, 1, 1, 1, 9, 9, 9, 9, 9, 1, 1, 5, 21, 21, 31, 31, 2, 2, 2, 1] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 19, 20, 21, 27, 28, 37] 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, 36]) total number of confs: 293 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567690 none CCOC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', '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, 5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 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, 133, 133, 133, 133, 133, 87, 133, 133, 24, 8, 1, 1, 1, 1, 1, 1, 1, 133, 133, 133, 201, 201, 201, 201, 201, 133, 133, 87, 24, 24, 8, 8, 133, 133, 133, 133] 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: 677 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567690 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567690 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567690/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567690 Building REAL300025567691 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567691' /scratch/stefan/7901150/working/building/REAL300025567691 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567691 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567691/0 /scratch/stefan/7901150/working/building/REAL300025567691 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 201) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/201 `/scratch/stefan/7901150/working/3D/201' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C)C2=NC=C(S(=O)(=O)NCCC3=NC(=O)O[N-]3)C=C12) `REAL300025567691.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567691.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567691/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567691 none CC1=NN(C)C2=NC=C(S(=O)(=O)NCCC3=NC(=O)O[N-]3)C=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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: [5, 1, 8, 8, 5, 1, 8, 1, 1, 14, 11, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 6, 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, 1, 2, 2, 2, 9, 54, 87, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 2, 2, 2, 1, 9, 54, 54, 87, 87, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 35, 21, 22, 29] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34]) total number of confs: 566 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567691 none CC1=NN(C)C2=NC=C(S(=O)(=O)NCCC3=NC(=O)O[N-]3)C=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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: [5, 1, 8, 8, 5, 1, 8, 1, 1, 14, 11, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 6, 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, 133, 82, 133, 133, 24, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 82, 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]) total number of confs: 669 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567691 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567691 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567691/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567691 Building REAL300025567692 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567692' /scratch/stefan/7901150/working/building/REAL300025567692 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567692 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567692/0 /scratch/stefan/7901150/working/building/REAL300025567692 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 202) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/202 `/scratch/stefan/7901150/working/3D/202' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=C(C(=O)OC)S1) `REAL300025567692.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567692/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567692 none COC(=O)C1=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=C(C(=O)OC)S1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 11, 12, 5, 14, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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, 4, 1, 1, 1, 1, 5, 5, 5, 9, 35, 35, 77, 77, 77, 77, 77, 1, 1, 11, 11, 11, 1, 5, 5, 5, 1, 9, 35, 35, 35, 35, 11, 11, 11] 201 rigid atoms, others: [2, 4, 5, 6, 7, 19, 20, 24, 28] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 233 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567692 none COC(=O)C1=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=C(C(=O)OC)S1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 11, 12, 5, 14, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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, 77, 127, 77, 77, 56, 36, 56, 56, 8, 8, 1, 1, 1, 1, 1, 1, 1, 77, 77, 125, 125, 125, 77, 127, 127, 127, 77, 36, 8, 8, 8, 8, 125, 125, 125] 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: 628 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567692 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567692 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567692/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567692 Building REAL300025567693 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567693' /scratch/stefan/7901150/working/building/REAL300025567693 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567693 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567693/0 /scratch/stefan/7901150/working/building/REAL300025567693 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 203) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/203 `/scratch/stefan/7901150/working/3D/203' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)CC2=CC=C(Cl)C(Cl)=C2)[N-]O1) `REAL300025567693.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567693.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567693/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567693 none O=C1N=C(CCNS(=O)(=O)CC2=CC=C(Cl)C(Cl)=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 5, 1, 1, 1, 1, 16, 1, 16, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 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: [1, 1, 1, 1, 1, 8, 22, 71, 94, 94, 94, 123, 200, 201, 201, 201, 201, 201, 200, 1, 1, 8, 8, 22, 22, 71, 123, 123, 201, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 19, 20] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 676 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567693 none O=C1N=C(CCNS(=O)(=O)CC2=CC=C(Cl)C(Cl)=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 5, 1, 1, 1, 1, 16, 1, 16, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 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: [201, 201, 201, 115, 97, 41, 14, 6, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 115, 115, 97, 97, 41, 6, 6, 1, 1, 1] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 652 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567693 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567693 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567693/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567693 Building REAL300025567694 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567694' /scratch/stefan/7901150/working/building/REAL300025567694 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567694 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567694/0 /scratch/stefan/7901150/working/building/REAL300025567694 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 204) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/204 `/scratch/stefan/7901150/working/3D/204' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C2=CC=C(Cl)N=C2C=C1) `REAL300025567694.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567694/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567694 none COC1=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C2=CC=C(Cl)N=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 16, 8, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 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] 0 hydrogens 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, 7, 7, 7, 12, 54, 80, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 12, 54, 54, 80, 80, 1, 1, 1, 1] 201 rigid atoms, others: [1, 2, 3, 4, 35, 33, 34, 16, 17, 18, 19, 20, 21, 22, 23, 24, 36] set([0, 32, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 533 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567694 none COC1=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C2=CC=C(Cl)N=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 16, 8, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 177, 90, 177, 177, 24, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 90, 24, 24, 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]) total number of confs: 732 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567694 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567694 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567694/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567694 Building REAL300025567695 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567695' /scratch/stefan/7901150/working/building/REAL300025567695 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567695 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567695/0 /scratch/stefan/7901150/working/building/REAL300025567695 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 205) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/205 `/scratch/stefan/7901150/working/3D/205' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2=CC=CC=C2OC(F)F)[N-]O1) `REAL300025567695.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567695.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567695/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567695 none O=C1N=C(CCNS(=O)(=O)C2=CC=CC=C2OC(F)F)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 3, 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: [1, 1, 1, 1, 1, 9, 17, 60, 113, 113, 113, 141, 141, 121, 141, 141, 141, 185, 201, 201, 1, 1, 9, 9, 17, 17, 60, 141, 141, 141, 141, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 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: 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567695 none O=C1N=C(CCNS(=O)(=O)C2=CC=CC=C2OC(F)F)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 3, 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: [141, 141, 141, 61, 53, 15, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 5, 17, 17, 141, 141, 61, 61, 53, 53, 15, 1, 1, 1, 1, 17] 201 rigid atoms, others: [7, 10, 11, 12, 13, 14, 15, 16, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31]) total number of confs: 429 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567695 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567695 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567695/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567695 Building REAL300025567696 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567696' /scratch/stefan/7901150/working/building/REAL300025567696 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567696 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567696/0 /scratch/stefan/7901150/working/building/REAL300025567696 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 206) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/206 `/scratch/stefan/7901150/working/3D/206' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2=CC=CC3=C2OCCO3)[N-]O1) `REAL300025567696.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567696.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567696/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567696 none O=C1N=C(CCNS(=O)(=O)C2=CC=CC3=C2OCCO3)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 12, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 3, 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: [1, 1, 1, 1, 1, 9, 25, 89, 153, 153, 153, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 9, 9, 25, 25, 89, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 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, 32, 33]) total number of confs: 706 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567696 none O=C1N=C(CCNS(=O)(=O)C2=CC=CC3=C2OCCO3)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 12, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 3, 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: [201, 201, 201, 101, 69, 19, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 101, 101, 69, 69, 19, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 604 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567696 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567696 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567696/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567696 Building REAL300025567697 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567697' /scratch/stefan/7901150/working/building/REAL300025567697 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567697 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567697/0 /scratch/stefan/7901150/working/building/REAL300025567697 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 207) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/207 `/scratch/stefan/7901150/working/3D/207' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C1=CC=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=C1) `REAL300025567697.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567697.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567697/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567697 none CCOC(=O)C1=CC=CC(S(=O)(=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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 5, 12, 1, 11, 1, 1, 1, 1, 1, 14, 11, 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, 3, 7, 5, 7, 7, 7, 7, 7, 7, 6, 6, 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: [12, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 29, 45, 119, 119, 119, 119, 119, 1, 13, 13, 13, 12, 12, 1, 1, 1, 9, 29, 29, 45, 45, 1] 201 rigid atoms, others: [3, 36, 5, 6, 7, 8, 9, 10, 22, 28, 29, 30] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 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 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567697 none CCOC(=O)C1=CC=CC(S(=O)(=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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 5, 12, 1, 11, 1, 1, 1, 1, 1, 14, 11, 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, 3, 7, 5, 7, 7, 7, 7, 7, 7, 6, 6, 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, 185, 185, 119, 185, 119, 119, 119, 119, 65, 47, 65, 65, 16, 8, 1, 1, 1, 1, 1, 1, 1, 119, 201, 201, 201, 201, 201, 119, 119, 119, 47, 16, 16, 8, 8, 119] 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: 703 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567697 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567697 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567697/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567697 Building REAL300025567698 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567698' /scratch/stefan/7901150/working/building/REAL300025567698 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567698 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567698/0 /scratch/stefan/7901150/working/building/REAL300025567698 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 208) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/208 `/scratch/stefan/7901150/working/3D/208' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOC(=O)C1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1) `REAL300025567698.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567698.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567698/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567698 none CCCOC(=O)C1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.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, 12, 1, 11, 1, 1, 1, 1, 14, 11, 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, 5, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 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: [18, 10, 3, 3, 1, 3, 1, 1, 1, 1, 1, 2, 2, 2, 7, 21, 33, 103, 103, 103, 103, 103, 1, 1, 18, 17, 17, 18, 18, 9, 9, 1, 1, 7, 21, 21, 33, 33, 1, 1] 201 rigid atoms, others: [32, 4, 38, 6, 7, 8, 9, 10, 39, 22, 23, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37]) total number of confs: 324 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567698 none CCCOC(=O)C1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.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, 12, 1, 11, 1, 1, 1, 1, 14, 11, 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, 5, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 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, 113, 103, 113, 67, 103, 103, 67, 53, 67, 67, 15, 7, 1, 1, 1, 1, 1, 1, 1, 103, 103, 201, 201, 201, 201, 201, 201, 201, 103, 103, 53, 16, 16, 7, 7, 103, 103] 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: 964 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567698 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567698 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567698/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567698 Building REAL300025567699 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567699' /scratch/stefan/7901150/working/building/REAL300025567699 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567699 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567699/0 /scratch/stefan/7901150/working/building/REAL300025567699 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 209) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/209 `/scratch/stefan/7901150/working/3D/209' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2=CC(Br)=CC=C2Cl)[N-]O1) `REAL300025567699.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567699.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567699/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567699 none O=C1N=C(CCNS(=O)(=O)C2=CC(Br)=CC=C2Cl)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 17, 1, 1, 1, 16, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 183 conformations in input total number of sets (complete confs): 183 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 9, 23, 99, 172, 172, 172, 183, 183, 183, 183, 183, 183, 183, 1, 1, 9, 9, 23, 23, 99, 183, 183, 183] 183 rigid atoms, others: [0, 1, 2, 3, 4, 18, 19] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 686 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567699 none O=C1N=C(CCNS(=O)(=O)C2=CC(Br)=CC=C2Cl)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 17, 1, 1, 1, 16, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 183 conformations in input total number of sets (complete confs): 183 using faster count positions algorithm for large data unique positions, atoms: [183, 183, 183, 87, 59, 15, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 183, 183, 87, 87, 59, 59, 15, 1, 1, 1] 183 rigid atoms, others: [7, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 522 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567699 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567699 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567699/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567699 Building REAL300025567700 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567700' /scratch/stefan/7901150/working/building/REAL300025567700 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567700 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567700/0 /scratch/stefan/7901150/working/building/REAL300025567700 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 210) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/210 `/scratch/stefan/7901150/working/3D/210' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C(=O)NC(=O)C2=CC(S(=O)(=O)NCCC3=NC(=O)O[N-]3)=CN=C21) `REAL300025567700.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567700.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567700/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567700 none CN1C(=O)NC(=O)C2=CC(S(=O)(=O)NCCC3=NC(=O)O[N-]3)=CN=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 8, 1, 11, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 1, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 6, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 55, 91, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 1, 9, 55, 55, 91, 91, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 35, 22, 23, 24, 25, 26, 27, 28, 29] set([32, 33, 34, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31]) total number of confs: 561 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567700 none CN1C(=O)NC(=O)C2=CC(S(=O)(=O)NCCC3=NC(=O)O[N-]3)=CN=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 8, 1, 11, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 1, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 6, 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, 201, 201, 201, 201, 201, 201, 201, 201, 137, 92, 137, 137, 24, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 92, 24, 24, 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]) total number of confs: 667 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567700 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567700 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567700/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567700 Building REAL300025567701 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567701' /scratch/stefan/7901150/working/building/REAL300025567701 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567701 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567701/0 /scratch/stefan/7901150/working/building/REAL300025567701 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 211) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/211 `/scratch/stefan/7901150/working/3D/211' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)CC2=CC=C(F)C=C2Br)[N-]O1) `REAL300025567701.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567701.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567701/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567701 none O=C1N=C(CCNS(=O)(=O)CC2=CC=C(F)C=C2Br)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 5, 1, 1, 1, 1, 15, 1, 1, 17, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 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: [1, 1, 1, 1, 1, 8, 21, 73, 109, 109, 109, 142, 201, 201, 201, 201, 201, 201, 201, 1, 1, 8, 8, 21, 21, 73, 142, 142, 201, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 19, 20] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 721 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567701 none O=C1N=C(CCNS(=O)(=O)CC2=CC=C(F)C=C2Br)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 5, 1, 1, 1, 1, 15, 1, 1, 17, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 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: [201, 201, 201, 121, 100, 37, 12, 4, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 121, 121, 100, 100, 37, 4, 4, 1, 1, 1] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 676 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567701 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567701 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567701/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567701 Building REAL300025567702 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567702' /scratch/stefan/7901150/working/building/REAL300025567702 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567702 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567702/0 /scratch/stefan/7901150/working/building/REAL300025567702 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 212) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/212 `/scratch/stefan/7901150/working/3D/212' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1=CC=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=C1) `REAL300025567702.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567702.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567702/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567702 none COCC1=CC=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 5, 1, 1, 1, 1, 1, 14, 11, 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, 6, 6, 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, 7, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 25, 43, 119, 119, 119, 119, 119, 1, 16, 16, 16, 7, 7, 1, 1, 1, 9, 25, 25, 43, 43, 1] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 34, 20, 26, 27, 28] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33]) total number of confs: 347 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567702 none COCC1=CC=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 5, 1, 1, 1, 1, 1, 14, 11, 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, 6, 6, 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, 119, 119, 92, 119, 119, 78, 57, 78, 78, 18, 8, 1, 1, 1, 1, 1, 1, 1, 119, 201, 201, 201, 201, 201, 117, 119, 119, 57, 18, 18, 8, 8, 119] 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: 952 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567702 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567702 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567702/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567702 Building REAL300025567703 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567703' /scratch/stefan/7901150/working/building/REAL300025567703 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567703 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567703/0 /scratch/stefan/7901150/working/building/REAL300025567703 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 213) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/213 `/scratch/stefan/7901150/working/3D/213' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C(F)C=C1S(=O)(=O)NCCC1=NC(=O)O[N-]1) `REAL300025567703.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567703.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567703/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567703 none COC(=O)C1=CC=C(F)C=C1S(=O)(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.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, 11, 1, 1, 1, 1, 15, 1, 1, 14, 11, 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, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 9, 41, 63, 138, 138, 138, 138, 138, 7, 7, 7, 1, 1, 1, 9, 41, 41, 63, 63] 201 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 11, 26, 27, 28] set([0, 1, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33]) total number of confs: 421 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567703 none COC(=O)C1=CC=C(F)C=C1S(=O)(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.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, 11, 1, 1, 1, 1, 15, 1, 1, 14, 11, 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, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 138, 201, 138, 138, 138, 138, 138, 138, 109, 71, 109, 109, 22, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 138, 138, 138, 71, 23, 22, 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: 746 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567703 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567703 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567703/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567703 Building REAL300025567704 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567704' /scratch/stefan/7901150/working/building/REAL300025567704 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567704 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567704/0 /scratch/stefan/7901150/working/building/REAL300025567704 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 214) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/214 `/scratch/stefan/7901150/working/3D/214' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2=CC3=C(C=C2[N+](=O)[O-])OCCO3)[N-]O1) `REAL300025567704.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567704.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567704/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567704 none O=C1N=C(CCNS(=O)(=O)C2=CC3=C(C=C2[N+](=O)[O-])OCCO3)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'O.3', 'C.3', 'C.3', 'O.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 8, 11, 11, 12, 5, 5, 12, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 3, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 107 conformations in input total number of sets (complete confs): 107 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 9, 23, 77, 107, 107, 107, 107, 107, 107, 107, 107, 107, 107, 107, 107, 107, 107, 107, 1, 1, 9, 9, 23, 23, 77, 107, 107, 107, 107, 107, 107] 107 rigid atoms, others: [0, 1, 2, 3, 4, 23, 24] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 394 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567704 none O=C1N=C(CCNS(=O)(=O)C2=CC3=C(C=C2[N+](=O)[O-])OCCO3)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'O.3', 'C.3', 'C.3', 'O.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 8, 11, 11, 12, 5, 5, 12, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 3, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 107 conformations in input total number of sets (complete confs): 107 using faster count positions algorithm for large data unique positions, atoms: [107, 107, 107, 47, 29, 5, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 107, 107, 47, 47, 29, 29, 5, 1, 1, 1, 1, 1, 1] 107 rigid atoms, others: [32, 33, 34, 35, 7, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 17, 18, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 305 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567704 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567704 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567704/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567704 Building REAL300025567705 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567705' /scratch/stefan/7901150/working/building/REAL300025567705 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567705 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567705/0 /scratch/stefan/7901150/working/building/REAL300025567705 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 215) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/215 `/scratch/stefan/7901150/working/3D/215' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2=CC(C(F)(F)F)=CC=C2F)[N-]O1) `REAL300025567705.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567705.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567705/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567705 none O=C1N=C(CCNS(=O)(=O)C2=CC(C(F)(F)F)=CC=C2F)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 15, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 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 201 conformations in 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, 23, 86, 132, 132, 132, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 9, 9, 23, 23, 86, 201, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 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]) total number of confs: 635 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567705 none O=C1N=C(CCNS(=O)(=O)C2=CC(C(F)(F)F)=CC=C2F)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 15, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 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 201 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, 81, 23, 7, 1, 7, 7, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 201, 201, 104, 104, 81, 81, 23, 1, 1, 1] 201 rigid atoms, others: [7, 10, 11, 12, 13, 17, 18, 19, 20, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 616 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567705 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567705 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567705/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567705 Building REAL300025567706 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567706' /scratch/stefan/7901150/working/building/REAL300025567706 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025567706 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567706/0 /scratch/stefan/7901150/working/building/REAL300025567706 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 216) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/216 `/scratch/stefan/7901150/working/3D/216' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2=CC(Br)=C(F)C=C2F)[N-]O1) `REAL300025567706.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567706.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567706/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567706 none O=C1N=C(CCNS(=O)(=O)C2=CC(Br)=C(F)C=C2F)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 17, 1, 15, 1, 1, 15, 8, 12, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 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: [1, 1, 1, 1, 1, 9, 25, 80, 139, 139, 139, 201, 201, 201, 193, 201, 201, 201, 201, 1, 1, 9, 9, 25, 25, 80, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 19, 20] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 718 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567706 none O=C1N=C(CCNS(=O)(=O)C2=CC(Br)=C(F)C=C2F)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 17, 1, 15, 1, 1, 15, 8, 12, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 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: [201, 201, 201, 101, 71, 23, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 101, 101, 71, 71, 23, 1, 1] 201 rigid atoms, others: [7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 602 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567706 /scratch/stefan/7901150/working /scratch/stefan/7901150 mkdir: created directory `1' /scratch/stefan/7901150/working/building/REAL300025567706/1 /scratch/stefan/7901150/working/building/REAL300025567706 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 1 (index: 217) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/217 `/scratch/stefan/7901150/working/3D/217' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CC[N-]S(=O)(=O)C2=CC(Br)=C(F)C=C2F)[N-]O1) `REAL300025567706.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025567706.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567706/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567706 none O=C1N=C(CC[N-]S(=O)(=O)C2=CC(Br)=C(F)C=C2F)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 17, 1, 15, 1, 1, 15, 8, 12, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 9, 11, 34, 87, 87, 87, 134, 134, 134, 124, 124, 134, 134, 134, 1, 1, 9, 9, 11, 11, 134, 134] 134 rigid atoms, others: [0, 1, 2, 3, 4, 19, 20] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26]) total number of confs: 425 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567706 none O=C1N=C(CC[N-]S(=O)(=O)C2=CC(Br)=C(F)C=C2F)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 17, 1, 15, 1, 1, 15, 8, 12, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 76, 72, 23, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 134, 134, 76, 76, 72, 72, 1, 1] 134 rigid atoms, others: [7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 19, 20, 21, 22, 23, 24]) total number of confs: 377 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567706 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567706 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 1: /scratch/stefan/7901150/working/building/REAL300025567706/1.* 0: /scratch/stefan/7901150/working/building/REAL300025567706/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567706 Building REAL300025567707 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567707' /scratch/stefan/7901150/working/building/REAL300025567707 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567707 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567707/0 /scratch/stefan/7901150/working/building/REAL300025567707 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 218) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/218 `/scratch/stefan/7901150/working/3D/218' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2=CC=C(F)C=C2C(F)(F)F)[N-]O1) `REAL300025567707.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567707.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567707/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567707 none O=C1N=C(CCNS(=O)(=O)C2=CC=C(F)C=C2C(F)(F)F)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 15, 1, 1, 5, 15, 15, 15, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 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 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, 9, 25, 81, 115, 115, 115, 115, 115, 115, 115, 115, 115, 115, 115, 115, 115, 1, 1, 9, 9, 25, 25, 81, 115, 115, 115] 115 rigid atoms, others: [0, 1, 2, 3, 4, 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]) total number of confs: 456 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567707 none O=C1N=C(CCNS(=O)(=O)C2=CC=C(F)C=C2C(F)(F)F)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 15, 1, 1, 5, 15, 15, 15, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 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 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, 51, 27, 5, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 115, 115, 51, 51, 27, 27, 5, 1, 1, 1] 115 rigid atoms, others: [7, 10, 11, 12, 13, 14, 15, 16, 17, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 340 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567707 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567707 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567707/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567707 Building REAL300025567708 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567708' /scratch/stefan/7901150/working/building/REAL300025567708 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567708 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567708/0 /scratch/stefan/7901150/working/building/REAL300025567708 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 219) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/219 `/scratch/stefan/7901150/working/3D/219' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)CC2=CC(C3=CC=CC=C3)=NO2)[N-]O1) `REAL300025567708.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567708.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567708/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567708 none O=C1N=C(CCNS(=O)(=O)CC2=CC(C3=CC=CC=C3)=NO2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'O.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 12, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in 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, 23, 62, 77, 77, 77, 103, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 9, 9, 23, 23, 62, 103, 103, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 22, 23] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 594 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567708 none O=C1N=C(CCNS(=O)(=O)CC2=CC(C3=CC=CC=C3)=NO2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'O.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 12, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 87, 70, 32, 15, 7, 15, 15, 1, 1, 1, 1, 1, 4, 4, 2, 4, 4, 1, 1, 201, 201, 87, 87, 70, 70, 32, 7, 7, 1, 4, 4, 2, 4, 4] 201 rigid atoms, others: [10, 11, 12, 13, 14, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36]) 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567708 none O=C1N=C(CCNS(=O)(=O)CC2=CC(C3=CC=CC=C3)=NO2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'O.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 12, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 119, 102, 58, 32, 18, 32, 32, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 201, 201, 119, 119, 102, 102, 58, 18, 18, 4, 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: 681 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567708 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567708 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567708/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567708 Building REAL300025567709 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567709' /scratch/stefan/7901150/working/building/REAL300025567709 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567709 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567709/0 /scratch/stefan/7901150/working/building/REAL300025567709 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 220) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/220 `/scratch/stefan/7901150/working/3D/220' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)CC2=CC=C(Cl)N=C2)[N-]O1) `REAL300025567709.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567709.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567709/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567709 none O=C1N=C(CCNS(=O)(=O)CC2=CC=C(Cl)N=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 5, 1, 1, 1, 1, 16, 8, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 8, 22, 67, 81, 81, 81, 127, 201, 201, 201, 201, 201, 201, 1, 1, 8, 8, 22, 22, 67, 127, 127, 201, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 18, 19] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 664 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567709 none O=C1N=C(CCNS(=O)(=O)CC2=CC=C(Cl)N=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 5, 1, 1, 1, 1, 16, 8, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 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, 201, 201, 123, 109, 47, 16, 6, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 123, 123, 109, 109, 47, 6, 6, 1, 1, 1] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 663 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567709 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567709 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567709/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567709 Building REAL300025567710 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567710' /scratch/stefan/7901150/working/building/REAL300025567710 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567710 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567710/0 /scratch/stefan/7901150/working/building/REAL300025567710 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 221) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/221 `/scratch/stefan/7901150/working/3D/221' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C1=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=CC=C1F) `REAL300025567710.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567710.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567710/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567710 none CCOC(=O)C1=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=CC=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 15, 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, 6, 6, 4, 7, 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: [18, 7, 6, 1, 6, 1, 1, 1, 1, 3, 3, 3, 9, 29, 37, 85, 85, 85, 85, 85, 1, 1, 1, 1, 18, 18, 18, 18, 18, 1, 9, 29, 29, 37, 37, 1, 1] 201 rigid atoms, others: [3, 36, 5, 6, 7, 8, 35, 20, 21, 22, 23, 29] set([0, 1, 2, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 30, 31, 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 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567710 none CCOC(=O)C1=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=CC=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 15, 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, 6, 6, 4, 7, 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, 194, 194, 85, 194, 85, 85, 53, 37, 53, 53, 14, 8, 1, 1, 1, 1, 1, 1, 1, 85, 85, 85, 85, 201, 201, 201, 201, 201, 85, 37, 15, 15, 8, 8, 85, 85] 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: 659 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567710 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567710 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567710/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567710 Building REAL300025567711 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567711' /scratch/stefan/7901150/working/building/REAL300025567711 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567711 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567711/0 /scratch/stefan/7901150/working/building/REAL300025567711 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 222) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/222 `/scratch/stefan/7901150/working/3D/222' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2=CC(F)=CC=C2Cl)[N-]O1) `REAL300025567711.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567711.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567711/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567711 none O=C1N=C(CCNS(=O)(=O)C2=CC(F)=CC=C2Cl)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 15, 1, 1, 1, 16, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [1, 1, 1, 1, 1, 9, 21, 98, 164, 164, 164, 175, 175, 175, 175, 175, 175, 175, 1, 1, 9, 9, 21, 21, 98, 175, 175, 175] 175 rigid atoms, others: [0, 1, 2, 3, 4, 18, 19] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 646 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567711 none O=C1N=C(CCNS(=O)(=O)C2=CC(F)=CC=C2Cl)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 15, 1, 1, 1, 16, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 175 conformations in input total number of sets (complete confs): 175 using faster count positions algorithm for large data unique positions, atoms: [175, 175, 175, 80, 56, 15, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 175, 175, 80, 80, 56, 56, 15, 1, 1, 1] 175 rigid atoms, others: [7, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 486 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567711 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567711 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567711/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567711 Building REAL300025567712 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567712' /scratch/stefan/7901150/working/building/REAL300025567712 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567712 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567712/0 /scratch/stefan/7901150/working/building/REAL300025567712 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 223) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/223 `/scratch/stefan/7901150/working/3D/223' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2=C(Cl)N=C3SC=CN32)[N-]O1) `REAL300025567712.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567712/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567712 none O=C1N=C(CCNS(=O)(=O)C2=C(Cl)N=C3SC=CN32)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'Cl', 'N.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.pl3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 16, 8, 1, 14, 1, 1, 8, 8, 12, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 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: [1, 1, 1, 1, 1, 9, 25, 84, 140, 140, 140, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 9, 9, 25, 25, 84, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 19, 20] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 644 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567712 none O=C1N=C(CCNS(=O)(=O)C2=C(Cl)N=C3SC=CN32)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'Cl', 'N.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.pl3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 16, 8, 1, 14, 1, 1, 8, 8, 12, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 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: [201, 201, 201, 96, 84, 23, 9, 1, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 96, 96, 84, 84, 23, 1, 1] 201 rigid atoms, others: [7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 568 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567712 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567712 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567712/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567712 Building REAL300025567713 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567713' /scratch/stefan/7901150/working/building/REAL300025567713 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025567713 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567713/0 /scratch/stefan/7901150/working/building/REAL300025567713 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 224) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/224 `/scratch/stefan/7901150/working/3D/224' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2=CC=C(Br)C=C2[N+](=O)[O-])[N-]O1) `REAL300025567713.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567713.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567713/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567713 none O=C1N=C(CCNS(=O)(=O)C2=CC=C(Br)C=C2[N+](=O)[O-])[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 17, 1, 1, 8, 11, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 3, 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: [1, 1, 1, 1, 1, 9, 23, 74, 96, 96, 96, 96, 96, 96, 96, 96, 96, 96, 96, 96, 1, 1, 9, 9, 23, 23, 74, 96, 96, 96] 96 rigid atoms, others: [0, 1, 2, 3, 4, 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]) total number of confs: 370 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567713 none O=C1N=C(CCNS(=O)(=O)C2=CC=C(Br)C=C2[N+](=O)[O-])[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 17, 1, 1, 8, 11, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 96 conformations in input total number of sets (complete confs): 96 using faster count positions algorithm for large data unique positions, atoms: [96, 96, 96, 45, 29, 5, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 96, 96, 45, 45, 29, 29, 5, 1, 1, 1] 96 rigid atoms, others: [7, 10, 11, 12, 13, 14, 15, 16, 17, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 288 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567713 /scratch/stefan/7901150/working /scratch/stefan/7901150 mkdir: created directory `1' /scratch/stefan/7901150/working/building/REAL300025567713/1 /scratch/stefan/7901150/working/building/REAL300025567713 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 1 (index: 225) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/225 `/scratch/stefan/7901150/working/3D/225' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CC[N-]S(=O)(=O)C2=CC=C(Br)C=C2[N+](=O)[O-])[N-]O1) `REAL300025567713.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025567713.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567713/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567713 none O=C1N=C(CC[N-]S(=O)(=O)C2=CC=C(Br)C=C2[N+](=O)[O-])[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 17, 1, 1, 8, 11, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 9, 15, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 9, 9, 15, 15, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 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]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567713 none O=C1N=C(CC[N-]S(=O)(=O)C2=CC=C(Br)C=C2[N+](=O)[O-])[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 17, 1, 1, 8, 11, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 25, 21, 5, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 50, 50, 25, 25, 21, 21, 1, 1, 1] 50 rigid atoms, others: [7, 10, 11, 12, 13, 14, 15, 16, 17, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 143 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567713 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567713 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 1: /scratch/stefan/7901150/working/building/REAL300025567713/1.* 0: /scratch/stefan/7901150/working/building/REAL300025567713/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567713 Building REAL300025567714 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567714' /scratch/stefan/7901150/working/building/REAL300025567714 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567714 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567714/0 /scratch/stefan/7901150/working/building/REAL300025567714 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 226) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/226 `/scratch/stefan/7901150/working/3D/226' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2=CC=C3COCC3=C2)[N-]O1) `REAL300025567714.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567714.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567714/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567714 none O=C1N=C(CCNS(=O)(=O)C2=CC=C3COCC3=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 5, 12, 5, 1, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 3, 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: [1, 1, 1, 1, 1, 9, 25, 88, 130, 130, 130, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 9, 9, 25, 25, 88, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 19, 20] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 651 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567714 none O=C1N=C(CCNS(=O)(=O)C2=CC=C3COCC3=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 5, 12, 5, 1, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 3, 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: [201, 201, 201, 93, 54, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 93, 93, 54, 54, 9, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 578 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567714 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567714 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567714/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567714 Building REAL300025567715 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567715' /scratch/stefan/7901150/working/building/REAL300025567715 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567715 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567715/0 /scratch/stefan/7901150/working/building/REAL300025567715 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 227) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/227 `/scratch/stefan/7901150/working/3D/227' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=CC(CS(=O)(=O)NCCC2=NC(=O)O[N-]2)=C1) `REAL300025567715.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567715.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567715/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567715 none COC(=O)C1=CC=CC(CS(=O)(=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', 'C.ar', 'C.ar', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 11, 1, 1, 1, 1, 1, 5, 14, 11, 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, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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, 6, 1, 6, 1, 1, 1, 1, 1, 1, 7, 15, 15, 15, 40, 69, 69, 161, 161, 161, 161, 161, 1, 6, 6, 6, 1, 1, 1, 7, 7, 40, 69, 69, 69, 69, 1] 201 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 22, 36, 26, 27, 28] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 431 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567715 none COC(=O)C1=CC=CC(CS(=O)(=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', 'C.ar', 'C.ar', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 11, 1, 1, 1, 1, 1, 5, 14, 11, 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, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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, 161, 201, 161, 161, 161, 161, 100, 60, 44, 60, 60, 20, 7, 1, 1, 1, 1, 1, 1, 1, 161, 201, 201, 201, 161, 161, 161, 100, 100, 44, 20, 20, 7, 7, 161] 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: 717 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567715 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567715 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567715/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567715 Building REAL300025567716 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567716' /scratch/stefan/7901150/working/building/REAL300025567716 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567716 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567716/0 /scratch/stefan/7901150/working/building/REAL300025567716 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 228) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/228 `/scratch/stefan/7901150/working/3D/228' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC(C2=CC=C(S(=O)(=O)NCCC3=NC(=O)O[N-]3)C=C2)=CO1) `REAL300025567716.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567716.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567716/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567716 none CC1=NC(C2=CC=C(S(=O)(=O)NCCC3=NC(=O)O[N-]3)C=C2)=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.2', 'O.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, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 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, 6, 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] 0 hydrogens need rotated 201 conformations in 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, 10, 10, 10, 25, 71, 103, 201, 201, 201, 201, 201, 6, 6, 1, 1, 2, 2, 2, 6, 6, 25, 71, 71, 103, 103, 6, 6, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 22, 23, 36] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 638 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567716 none CC1=NC(C2=CC=C(S(=O)(=O)NCCC3=NC(=O)O[N-]3)C=C2)=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.2', 'O.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, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 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, 6, 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] 0 hydrogens need rotated 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, 2, 2, 2, 9, 35, 68, 191, 191, 191, 191, 191, 1, 1, 6, 6, 7, 7, 7, 1, 1, 9, 35, 35, 68, 68, 1, 1, 6] 201 rigid atoms, others: [34, 3, 4, 5, 6, 7, 8, 35, 20, 21, 27, 28] 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, 36]) total number of confs: 487 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567716 none CC1=NC(C2=CC=C(S(=O)(=O)NCCC3=NC(=O)O[N-]3)C=C2)=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.2', 'O.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, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 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, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 139, 115, 191, 191, 115, 75, 115, 115, 22, 8, 1, 1, 1, 1, 1, 1, 1, 191, 191, 201, 201, 201, 201, 201, 191, 191, 75, 22, 22, 8, 8, 191, 191, 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: 988 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567716 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567716 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567716/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567716 Building REAL300025567717 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567717' /scratch/stefan/7901150/working/building/REAL300025567717 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567717 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567717/0 /scratch/stefan/7901150/working/building/REAL300025567717 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 229) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/229 `/scratch/stefan/7901150/working/3D/229' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)CCOCC(F)(F)F)[N-]O1) `REAL300025567717.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567717.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567717/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567717 none O=C1N=C(CCNS(=O)(=O)CCOCC(F)(F)F)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 5, 5, 12, 5, 5, 15, 15, 15, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 3, 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: [1, 1, 1, 1, 1, 9, 17, 46, 78, 78, 78, 103, 103, 201, 201, 201, 201, 201, 1, 1, 9, 9, 17, 17, 46, 103, 103, 103, 103, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 18, 19] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 614 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567717 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567717 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567717/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567717 Building REAL300025567718 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567718' /scratch/stefan/7901150/working/building/REAL300025567718 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567718 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567718/0 /scratch/stefan/7901150/working/building/REAL300025567718 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 230) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/230 `/scratch/stefan/7901150/working/3D/230' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)CCCS(=O)(=O)NCCC1=NC(=O)O[N-]1) `REAL300025567718.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567718.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567718/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567718 none CCOC(=O)CCCS(=O)(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', '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, 12, 1, 11, 5, 5, 5, 14, 11, 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, 3, 7, 5, 7, 7, 7, 7, 6, 6, 4, 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, 192, 192, 79, 192, 77, 71, 35, 27, 35, 35, 15, 7, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 79, 79, 77, 77, 71, 71, 27, 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: 772 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567718 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567718 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567718/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567718 Building REAL300025567719 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567719' /scratch/stefan/7901150/working/building/REAL300025567719 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567719 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567719/0 /scratch/stefan/7901150/working/building/REAL300025567719 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 231) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/231 `/scratch/stefan/7901150/working/3D/231' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC2=CC(S(=O)(=O)NCCC3=NC(=O)O[N-]3)=CC=C2O1) `REAL300025567719.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567719.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567719/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567719 none CC1CC2=CC(S(=O)(=O)NCCC3=NC(=O)O[N-]3)=CC=C2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 12, 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, 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, 1, 1, 2, 2, 2, 9, 54, 92, 201, 201, 201, 201, 201, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 9, 54, 54, 92, 92, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 34, 18, 19, 20, 21, 25, 26, 27, 28, 35] set([32, 33, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 29, 30, 31]) total number of confs: 577 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567719 none CC1CC2=CC(S(=O)(=O)NCCC3=NC(=O)O[N-]3)=CC=C2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 12, 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, 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, 201, 201, 126, 86, 126, 126, 24, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 86, 24, 24, 8, 8, 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]) total number of confs: 637 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567719 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567719 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567719/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567719 Building REAL300025567720 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567720' /scratch/stefan/7901150/working/building/REAL300025567720 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567720 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567720/0 /scratch/stefan/7901150/working/building/REAL300025567720 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 232) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/232 `/scratch/stefan/7901150/working/3D/232' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)CC2=C(Cl)C=CC=C2Cl)[N-]O1) `REAL300025567720.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567720.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567720/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567720 none O=C1N=C(CCNS(=O)(=O)CC2=C(Cl)C=CC=C2Cl)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 5, 1, 1, 16, 1, 1, 1, 1, 16, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 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: [1, 1, 1, 1, 1, 9, 25, 114, 187, 187, 187, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 9, 9, 25, 25, 114, 201, 201, 201, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 19, 20] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 782 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567720 none O=C1N=C(CCNS(=O)(=O)CC2=C(Cl)C=CC=C2Cl)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 5, 1, 1, 16, 1, 1, 1, 1, 16, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 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: [201, 201, 201, 113, 77, 19, 10, 2, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 113, 113, 77, 77, 19, 2, 2, 1, 1, 1] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 646 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567720 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567720 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567720/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567720 Building REAL300025567721 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567721' /scratch/stefan/7901150/working/building/REAL300025567721 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567721 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567721/0 /scratch/stefan/7901150/working/building/REAL300025567721 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 233) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/233 `/scratch/stefan/7901150/working/3D/233' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C2=CC=CC=C2S1) `REAL300025567721.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567721.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567721/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567721 none COC(=O)C1=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C2=CC=CC=C2S1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 6, 6, 4, 7, 7, 7, 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 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 1, 4, 1, 1, 1, 4, 4, 4, 5, 7, 7, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 5, 7, 7, 7, 7, 1, 1, 1, 1] 11 rigid atoms, others: [33, 2, 35, 4, 5, 6, 34, 18, 19, 20, 21, 22, 23, 24, 36] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 42 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567721 none COC(=O)C1=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C2=CC=CC=C2S1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 6, 6, 4, 7, 7, 7, 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 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 11, 11, 10, 11, 11, 9, 6, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 10, 9, 9, 6, 6, 11, 11, 11, 11] 11 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: 47 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567721 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567721 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567721/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567721 Building REAL300025567722 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567722' /scratch/stefan/7901150/working/building/REAL300025567722 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567722 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567722/0 /scratch/stefan/7901150/working/building/REAL300025567722 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 234) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/234 `/scratch/stefan/7901150/working/3D/234' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(OCC1=CC=CC=C1)N1CC[C@@H](S(=O)(=O)NCCC2=NC(=O)O[N-]2)C1) `REAL300025567722.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567722.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567722/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567722 none O=C(OCC1=CC=CC=C1)N1CC[C@@H](S(=O)(=O)NCCC2=NC(=O)O[N-]2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [11, 1, 12, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 7, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 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, 18, 3, 1, 1, 1, 1, 1, 1, 1, 18, 32, 32, 32, 32, 32, 69, 69, 69, 104, 126, 126, 201, 201, 201, 201, 201, 32, 3, 3, 1, 1, 1, 1, 1, 32, 32, 32, 32, 104, 126, 126, 126, 126, 32, 32] 201 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 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, 29, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 640 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567722 none O=C(OCC1=CC=CC=C1)N1CC[C@@H](S(=O)(=O)NCCC2=NC(=O)O[N-]2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [11, 1, 12, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 7, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 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, 2, 2, 14, 32, 32, 14, 32, 32, 1, 1, 1, 1, 1, 1, 7, 7, 7, 17, 28, 29, 68, 68, 68, 68, 68, 1, 14, 14, 32, 32, 14, 32, 32, 1, 1, 1, 1, 17, 28, 28, 29, 29, 1, 1] 201 rigid atoms, others: [1, 45, 35, 36, 37, 38, 44, 10, 11, 12, 13, 14, 15, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43]) total number of confs: 298 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567722 none O=C(OCC1=CC=CC=C1)N1CC[C@@H](S(=O)(=O)NCCC2=NC(=O)O[N-]2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [11, 1, 12, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 7, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 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: [99, 68, 99, 99, 201, 201, 201, 201, 201, 201, 68, 68, 68, 46, 68, 32, 46, 46, 14, 7, 1, 1, 1, 1, 1, 1, 1, 68, 201, 201, 201, 201, 201, 201, 201, 68, 68, 68, 68, 32, 14, 14, 7, 7, 68, 68] 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: 808 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567722 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567722 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567722/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567722 Building REAL300025567723 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567723' /scratch/stefan/7901150/working/building/REAL300025567723 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567723 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567723/0 /scratch/stefan/7901150/working/building/REAL300025567723 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 235) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/235 `/scratch/stefan/7901150/working/3D/235' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(OCC1=CC=CC=C1)N1CC[C@H](S(=O)(=O)NCCC2=NC(=O)O[N-]2)C1) `REAL300025567723.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567723.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567723/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567723 none O=C(OCC1=CC=CC=C1)N1CC[C@H](S(=O)(=O)NCCC2=NC(=O)O[N-]2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [11, 1, 12, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 7, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 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: [21, 18, 3, 1, 1, 1, 1, 1, 1, 1, 21, 37, 37, 37, 37, 37, 70, 70, 70, 106, 125, 125, 201, 201, 201, 201, 201, 37, 3, 3, 1, 1, 1, 1, 1, 37, 37, 37, 37, 106, 125, 125, 125, 125, 37, 37] 201 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 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, 29, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 623 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567723 none O=C(OCC1=CC=CC=C1)N1CC[C@H](S(=O)(=O)NCCC2=NC(=O)O[N-]2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [11, 1, 12, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 7, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 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, 2, 5, 17, 37, 37, 17, 37, 37, 1, 1, 1, 1, 1, 1, 7, 7, 7, 16, 26, 26, 60, 60, 60, 60, 60, 1, 17, 17, 37, 37, 17, 37, 37, 1, 1, 1, 1, 16, 26, 26, 26, 26, 1, 1] 201 rigid atoms, others: [1, 45, 35, 36, 37, 38, 44, 10, 11, 12, 13, 14, 15, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43]) total number of confs: 290 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567723 none O=C(OCC1=CC=CC=C1)N1CC[C@H](S(=O)(=O)NCCC2=NC(=O)O[N-]2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [11, 1, 12, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 7, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 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: [90, 60, 90, 93, 201, 201, 201, 201, 201, 201, 60, 60, 60, 40, 60, 30, 40, 40, 16, 7, 1, 1, 1, 1, 1, 1, 1, 60, 201, 201, 201, 201, 201, 201, 201, 60, 60, 60, 60, 30, 16, 16, 7, 7, 60, 60] 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: 793 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567723 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567723 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567723/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567723 Building REAL300025567724 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567724' /scratch/stefan/7901150/working/building/REAL300025567724 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567724 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567724/0 /scratch/stefan/7901150/working/building/REAL300025567724 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 236) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/236 `/scratch/stefan/7901150/working/3D/236' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C(F)=C1) `REAL300025567724.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567724.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567724/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567724 none CC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C(F)=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.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, 1, 1, 1, 14, 11, 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, 6, 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, 7, 7, 7, 21, 71, 100, 201, 201, 201, 201, 201, 1, 1, 1, 2, 2, 2, 1, 1, 21, 71, 71, 100, 100, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 17, 18, 19, 23, 24, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 25, 26, 27, 28, 29]) total number of confs: 609 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567724 none CC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C(F)=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.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, 1, 1, 1, 14, 11, 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, 6, 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, 146, 82, 146, 146, 23, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 82, 23, 23, 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]) total number of confs: 664 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567724 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567724 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567724/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567724 Building REAL300025567725 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567725' /scratch/stefan/7901150/working/building/REAL300025567725 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567725 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567725/0 /scratch/stefan/7901150/working/building/REAL300025567725 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 237) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/237 `/scratch/stefan/7901150/working/3D/237' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC1=CC(F)=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1Cl) `REAL300025567725.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567725.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567725/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567725 none CC(=O)NC1=CC(F)=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 15, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 16, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 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, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 15, 37, 59, 157, 157, 157, 157, 157, 1, 1, 1, 4, 4, 4, 4, 1, 15, 37, 37, 59, 59, 1] 201 rigid atoms, others: [34, 3, 4, 5, 6, 7, 8, 9, 21, 22, 23, 28] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 29, 30, 31, 32, 33]) total number of confs: 403 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567725 none CC(=O)NC1=CC(F)=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 15, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 16, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 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, 157, 157, 157, 157, 157, 121, 75, 121, 121, 24, 8, 1, 1, 1, 1, 1, 1, 1, 157, 157, 157, 201, 201, 201, 201, 157, 75, 24, 24, 8, 8, 157] 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: 733 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567725 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567725 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567725/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567725 Building REAL300025567726 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567726' /scratch/stefan/7901150/working/building/REAL300025567726 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567726 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567726/0 /scratch/stefan/7901150/working/building/REAL300025567726 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 238) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/238 `/scratch/stefan/7901150/working/3D/238' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCN(C)C(=O)C1=CC=CC=C1S(=O)(=O)NCCC1=NC(=O)O[N-]1) `REAL300025567726.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567726.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567726/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567726 none CCCCN(C)C(=O)C1=CC=CC=C1S(=O)(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', '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, 5, 1, 11, 1, 1, 1, 1, 1, 1, 14, 11, 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, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 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: [26, 26, 23, 11, 5, 11, 1, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 26, 26, 72, 72, 72, 72, 72, 26, 26, 26, 26, 26, 26, 26, 23, 23, 11, 11, 11, 1, 1, 1, 1, 7, 26, 26, 26, 26] 201 rigid atoms, others: [6, 38, 39, 8, 9, 10, 11, 12, 13, 14, 40, 41] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46]) total number of confs: 269 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567726 none CCCCN(C)C(=O)C1=CC=CC=C1S(=O)(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', '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, 5, 1, 11, 1, 1, 1, 1, 1, 1, 14, 11, 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, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 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, 131, 94, 131, 72, 94, 72, 72, 66, 72, 72, 66, 34, 66, 66, 9, 9, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 131, 131, 131, 72, 72, 72, 72, 34, 9, 9, 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: 883 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567726 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567726 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567726/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567726 Building REAL300025567727 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567727' /scratch/stefan/7901150/working/building/REAL300025567727 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567727 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567727/0 /scratch/stefan/7901150/working/building/REAL300025567727 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 239) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/239 `/scratch/stefan/7901150/working/3D/239' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2=CC=C(OC3=CC=CC=C3Cl)C=C2)[N-]O1) `REAL300025567727.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567727.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567727/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567727 none O=C1N=C(CCNS(=O)(=O)C2=CC=C(OC3=CC=CC=C3Cl)C=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 16, 1, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 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] 0 hydrogens need rotated 201 conformations in 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, 21, 46, 63, 63, 63, 63, 63, 63, 63, 171, 201, 201, 171, 201, 201, 201, 63, 63, 1, 1, 9, 9, 21, 21, 46, 63, 63, 201, 201, 201, 201, 63, 63] 201 rigid atoms, others: [0, 1, 2, 3, 4, 24, 25] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 599 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567727 none O=C1N=C(CCNS(=O)(=O)C2=CC=C(OC3=CC=CC=C3Cl)C=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 16, 1, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [63, 63, 63, 21, 13, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 8, 10, 10, 8, 10, 10, 10, 1, 1, 63, 63, 21, 21, 13, 13, 5, 1, 1, 10, 10, 10, 10, 1, 1] 201 rigid atoms, others: [32, 37, 38, 7, 10, 11, 12, 13, 14, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36]) 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567727 none O=C1N=C(CCNS(=O)(=O)C2=CC=C(OC3=CC=CC=C3Cl)C=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 16, 1, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 95, 67, 27, 10, 10, 10, 10, 8, 10, 10, 6, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 201, 201, 95, 95, 67, 67, 27, 10, 10, 1, 1, 1, 1, 10, 10] 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: 607 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567727 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567727 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567727/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567727 Building REAL300025567728 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567728' /scratch/stefan/7901150/working/building/REAL300025567728 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567728 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567728/0 /scratch/stefan/7901150/working/building/REAL300025567728 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 240) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/240 `/scratch/stefan/7901150/working/3D/240' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(Cl)=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1Cl) `REAL300025567728.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567728.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567728/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567728 none COC1=CC(Cl)=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 12, 1, 1, 1, 16, 1, 14, 11, 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, 3, 7, 7, 7, 7, 7, 7, 6, 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, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 30, 51, 182, 182, 182, 182, 182, 1, 1, 1, 3, 3, 3, 1, 5, 30, 30, 51, 51, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 25, 31] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 26, 27, 28, 29, 30]) total number of confs: 403 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567728 none COC1=CC(Cl)=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 12, 1, 1, 1, 16, 1, 14, 11, 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, 3, 7, 7, 7, 7, 7, 7, 6, 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, 182, 182, 182, 182, 182, 182, 106, 182, 182, 24, 8, 1, 1, 1, 1, 1, 1, 1, 182, 182, 182, 201, 201, 201, 182, 106, 25, 25, 8, 8, 182] 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: 726 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567728 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567728 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567728/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567728 Building REAL300025567729 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567729' /scratch/stefan/7901150/working/building/REAL300025567729 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567729 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567729/0 /scratch/stefan/7901150/working/building/REAL300025567729 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 241) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/241 `/scratch/stefan/7901150/working/3D/241' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=CC=C1F) `REAL300025567729.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567729/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567729 none CC1=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=CC=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 1, 1, 1, 14, 11, 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, 7, 7, 7, 6, 6, 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, 2, 2, 2, 9, 53, 95, 201, 201, 201, 201, 201, 1, 1, 1, 1, 2, 2, 2, 1, 9, 53, 53, 95, 95, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 16, 17, 18, 19, 23, 29, 30] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 24, 25, 26, 27, 28]) total number of confs: 593 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567729 none CC1=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=CC=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 1, 1, 1, 14, 11, 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, 7, 7, 7, 6, 6, 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, 107, 75, 107, 107, 24, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 75, 25, 25, 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]) total number of confs: 615 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567729 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567729 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567729/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567729 Building REAL300025567730 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567730' /scratch/stefan/7901150/working/building/REAL300025567730 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567730 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567730/0 /scratch/stefan/7901150/working/building/REAL300025567730 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 242) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/242 `/scratch/stefan/7901150/working/3D/242' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(N2C=C(S(=O)(=O)NCCC3=NC(=O)O[N-]3)C=N2)C=C1) `REAL300025567730.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567730.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567730/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567730 none CC1=CC=C(N2C=C(S(=O)(=O)NCCC3=NC(=O)O[N-]3)C=N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 1, 1, 1, 1, 8, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 1, 1, 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, 6, 6, 4, 7, 7, 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, 4, 4, 4, 9, 9, 9, 24, 81, 109, 201, 201, 201, 201, 201, 4, 4, 1, 1, 2, 2, 2, 1, 1, 5, 24, 81, 81, 109, 109, 4, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 22, 23, 36, 27, 28, 37] 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]) total number of confs: 626 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567730 none CC1=CC=C(N2C=C(S(=O)(=O)NCCC3=NC(=O)O[N-]3)C=N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 1, 1, 1, 1, 8, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 1, 1, 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, 6, 6, 4, 7, 7, 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, 3, 3, 1, 1, 1, 1, 1, 3, 3, 3, 9, 57, 99, 201, 201, 201, 201, 201, 1, 1, 3, 3, 4, 4, 4, 4, 4, 1, 9, 57, 57, 99, 99, 1, 4, 4] 201 rigid atoms, others: [35, 4, 5, 6, 7, 8, 20, 21, 29] set([0, 1, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 36, 37]) total number of confs: 636 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567730 none CC1=CC=C(N2C=C(S(=O)(=O)NCCC3=NC(=O)O[N-]3)C=N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 1, 1, 1, 1, 8, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 1, 1, 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, 6, 6, 4, 7, 7, 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, 158, 87, 158, 158, 24, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 87, 24, 24, 8, 8, 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]) total number of confs: 725 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567730 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567730 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567730/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567730 Building REAL300025567731 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567731' /scratch/stefan/7901150/working/building/REAL300025567731 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567731 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567731/0 /scratch/stefan/7901150/working/building/REAL300025567731 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 243) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/243 `/scratch/stefan/7901150/working/3D/243' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(OCC1=CC=CC=C1)N1CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C1) `REAL300025567731.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567731.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567731/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567731 none O=C(OCC1=CC=CC=C1)N1CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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: [11, 1, 12, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 14, 11, 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: [6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 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: [19, 17, 3, 1, 1, 1, 1, 1, 1, 1, 19, 34, 34, 33, 67, 67, 67, 112, 135, 136, 201, 201, 201, 201, 201, 34, 3, 3, 1, 1, 1, 1, 1, 34, 34, 34, 112, 135, 135, 136, 136, 34, 34] 201 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 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, 27, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 652 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567731 none O=C(OCC1=CC=CC=C1)N1CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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: [11, 1, 12, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 14, 11, 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: [6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 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, 5, 17, 34, 34, 21, 34, 34, 1, 1, 1, 1, 6, 6, 6, 16, 29, 31, 80, 80, 80, 80, 80, 1, 17, 17, 34, 34, 34, 34, 34, 1, 1, 1, 16, 29, 29, 31, 31, 1, 1] 201 rigid atoms, others: [1, 34, 35, 33, 41, 10, 11, 12, 13, 25, 42] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40]) total number of confs: 337 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567731 none O=C(OCC1=CC=CC=C1)N1CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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: [11, 1, 12, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 14, 11, 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: [6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 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: [104, 80, 104, 108, 201, 201, 201, 201, 201, 201, 80, 80, 41, 29, 41, 41, 13, 7, 1, 1, 1, 1, 1, 1, 1, 80, 201, 201, 201, 201, 201, 201, 201, 80, 80, 80, 29, 13, 13, 7, 7, 80, 80] 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: 801 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567731 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567731 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567731/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567731 Building REAL300025567732 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567732' /scratch/stefan/7901150/working/building/REAL300025567732 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025567732 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567732/0 /scratch/stefan/7901150/working/building/REAL300025567732 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 244) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/244 `/scratch/stefan/7901150/working/3D/244' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)O1) `REAL300025567732.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567732/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567732 none COC(=O)C1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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, 3, 1, 3, 1, 1, 1, 1, 1, 6, 6, 6, 19, 64, 86, 165, 165, 165, 165, 165, 1, 3, 3, 3, 1, 1, 19, 64, 64, 86, 86] 201 rigid atoms, others: [2, 4, 5, 6, 7, 8, 20, 24, 25] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 26, 27, 28, 29, 30]) total number of confs: 520 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567732 none COC(=O)C1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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, 201, 165, 201, 165, 165, 165, 77, 53, 77, 77, 18, 8, 1, 1, 1, 1, 1, 1, 1, 165, 201, 201, 201, 165, 165, 53, 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, 30]) total number of confs: 581 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567732 /scratch/stefan/7901150/working /scratch/stefan/7901150 mkdir: created directory `1' /scratch/stefan/7901150/working/building/REAL300025567732/1 /scratch/stefan/7901150/working/building/REAL300025567732 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 1 (index: 245) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/245 `/scratch/stefan/7901150/working/3D/245' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C(S(=O)(=O)[N-]CCC2=NC(=O)O[N-]2)O1) `REAL300025567732.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025567732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567732/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567732 none COC(=O)C1=CC=C(S(=O)(=O)[N-]CCC2=NC(=O)O[N-]2)O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', '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'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 5, 3, 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: [10, 10, 1, 10, 1, 1, 1, 1, 1, 6, 6, 6, 25, 77, 77, 152, 152, 152, 152, 152, 1, 11, 11, 11, 1, 1, 77, 77, 77, 77] 201 rigid atoms, others: [2, 4, 5, 6, 7, 8, 20, 24, 25] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 26, 27, 28, 29]) total number of confs: 422 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567732 none COC(=O)C1=CC=C(S(=O)(=O)[N-]CCC2=NC(=O)O[N-]2)O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', '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'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 5, 3, 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: [201, 201, 152, 201, 152, 152, 152, 94, 29, 94, 94, 8, 8, 1, 1, 1, 1, 1, 1, 1, 152, 201, 201, 201, 152, 152, 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: 625 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567732 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567732 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 1: /scratch/stefan/7901150/working/building/REAL300025567732/1.* 0: /scratch/stefan/7901150/working/building/REAL300025567732/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567732 Building REAL300025567733 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567733' /scratch/stefan/7901150/working/building/REAL300025567733 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567733 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567733/0 /scratch/stefan/7901150/working/building/REAL300025567733 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 246) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/246 `/scratch/stefan/7901150/working/3D/246' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2=CC=CC3=CC=CN=C32)[N-]O1) `REAL300025567733.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567733.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567733/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567733 none O=C1N=C(CCNS(=O)(=O)C2=CC=CC3=CC=CN=C32)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 9, 21, 85, 158, 158, 158, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 9, 9, 21, 21, 85, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 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, 32]) total number of confs: 701 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567733 none O=C1N=C(CCNS(=O)(=O)C2=CC=CC3=CC=CN=C32)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 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, 201, 201, 103, 71, 20, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 103, 103, 71, 71, 20, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 612 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567733 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567733 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567733/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567733 Building REAL300025567734 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567734' /scratch/stefan/7901150/working/building/REAL300025567734 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567734 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567734/0 /scratch/stefan/7901150/working/building/REAL300025567734 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 247) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/247 `/scratch/stefan/7901150/working/3D/247' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2=CSC(C3=CC=CC=C3)=N2)[N-]O1) `REAL300025567734.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567734/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567734 none O=C1N=C(CCNS(=O)(=O)C2=CSC(C3=CC=CC=C3)=N2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 14, 1, 1, 1, 1, 1, 1, 1, 8, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 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: [1, 1, 1, 1, 1, 9, 23, 77, 125, 125, 125, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 9, 9, 23, 23, 77, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 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]) total number of confs: 623 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567734 none O=C1N=C(CCNS(=O)(=O)C2=CSC(C3=CC=CC=C3)=N2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 14, 1, 1, 1, 1, 1, 1, 1, 8, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 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: [201, 201, 201, 98, 70, 24, 7, 1, 7, 7, 1, 1, 1, 1, 1, 3, 3, 1, 3, 3, 1, 201, 201, 98, 98, 70, 70, 24, 1, 3, 3, 1, 3, 3] 201 rigid atoms, others: [7, 10, 11, 12, 13, 14, 20, 28] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33]) total number of confs: 616 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567734 none O=C1N=C(CCNS(=O)(=O)C2=CSC(C3=CC=CC=C3)=N2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 14, 1, 1, 1, 1, 1, 1, 1, 8, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 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: [201, 201, 201, 128, 119, 55, 19, 3, 19, 19, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 201, 201, 128, 128, 119, 119, 55, 3, 1, 1, 1, 1, 1] 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]) total number of confs: 648 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567734 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567734 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567734/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567734 Building REAL300025567735 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567735' /scratch/stefan/7901150/working/building/REAL300025567735 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567735 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567735/0 /scratch/stefan/7901150/working/building/REAL300025567735 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 248) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/248 `/scratch/stefan/7901150/working/3D/248' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2=CSC(C3=CC=C(Cl)C=C3)=N2)[N-]O1) `REAL300025567735.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567735.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567735/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567735 none O=C1N=C(CCNS(=O)(=O)C2=CSC(C3=CC=C(Cl)C=C3)=N2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 14, 1, 1, 1, 1, 1, 16, 1, 1, 8, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 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 201 conformations in 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, 23, 73, 112, 112, 112, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 9, 9, 23, 23, 73, 201, 201, 201, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 22, 23] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 596 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567735 none O=C1N=C(CCNS(=O)(=O)C2=CSC(C3=CC=C(Cl)C=C3)=N2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 14, 1, 1, 1, 1, 1, 16, 1, 1, 8, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 99, 72, 24, 6, 1, 6, 6, 1, 1, 1, 1, 1, 4, 4, 2, 2, 4, 4, 1, 201, 201, 99, 99, 72, 72, 24, 1, 4, 4, 4, 4] 201 rigid atoms, others: [7, 10, 11, 12, 13, 14, 21, 29] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33]) 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567735 none O=C1N=C(CCNS(=O)(=O)C2=CSC(C3=CC=C(Cl)C=C3)=N2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 14, 1, 1, 1, 1, 1, 16, 1, 1, 8, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 120, 115, 58, 19, 4, 19, 19, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 201, 201, 120, 120, 115, 115, 58, 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: 616 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567735 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567735 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567735/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567735 Building REAL300025567736 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567736' /scratch/stefan/7901150/working/building/REAL300025567736 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567736 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567736/0 /scratch/stefan/7901150/working/building/REAL300025567736 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 249) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/249 `/scratch/stefan/7901150/working/3D/249' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2CC3=CC=CC=C3C2)[N-]O1) `REAL300025567736.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567736.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567736/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567736 none O=C1N=C(CCNS(=O)(=O)C2CC3=CC=CC=C3C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 5, 5, 1, 1, 1, 1, 1, 1, 5, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 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, 1, 9, 25, 93, 162, 162, 162, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 9, 9, 25, 25, 93, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 19, 20] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 783 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567736 none O=C1N=C(CCNS(=O)(=O)C2CC3=CC=CC=C3C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 5, 5, 1, 1, 1, 1, 1, 1, 5, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 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: [201, 201, 201, 115, 90, 31, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 115, 115, 90, 90, 31, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 618 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567736 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567736 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567736/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567736 Building REAL300025567737 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567737' /scratch/stefan/7901150/working/building/REAL300025567737 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025567737 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567737/0 /scratch/stefan/7901150/working/building/REAL300025567737 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 250) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/250 `/scratch/stefan/7901150/working/3D/250' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2=CC(F)=C(F)C=C2F)[N-]O1) `REAL300025567737.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567737.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567737/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567737 none O=C1N=C(CCNS(=O)(=O)C2=CC(F)=C(F)C=C2F)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 15, 1, 15, 1, 1, 15, 8, 12, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 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: [1, 1, 1, 1, 1, 9, 25, 82, 139, 139, 139, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 9, 9, 25, 25, 82, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 19, 20] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 670 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567737 none O=C1N=C(CCNS(=O)(=O)C2=CC(F)=C(F)C=C2F)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 15, 1, 15, 1, 1, 15, 8, 12, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 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: [201, 201, 201, 96, 66, 23, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 96, 96, 66, 66, 23, 1, 1] 201 rigid atoms, others: [7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 583 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567737 /scratch/stefan/7901150/working /scratch/stefan/7901150 mkdir: created directory `1' /scratch/stefan/7901150/working/building/REAL300025567737/1 /scratch/stefan/7901150/working/building/REAL300025567737 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 1 (index: 251) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/251 `/scratch/stefan/7901150/working/3D/251' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CC[N-]S(=O)(=O)C2=CC(F)=C(F)C=C2F)[N-]O1) `REAL300025567737.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025567737.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567737/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567737 none O=C1N=C(CC[N-]S(=O)(=O)C2=CC(F)=C(F)C=C2F)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 15, 1, 15, 1, 1, 15, 8, 12, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [1, 1, 1, 1, 1, 9, 13, 36, 87, 87, 87, 129, 129, 129, 129, 129, 129, 129, 129, 1, 1, 9, 9, 13, 13, 129, 129] 129 rigid atoms, others: [0, 1, 2, 3, 4, 19, 20] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 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 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567737 none O=C1N=C(CC[N-]S(=O)(=O)C2=CC(F)=C(F)C=C2F)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 15, 1, 15, 1, 1, 15, 8, 12, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [129, 129, 129, 74, 70, 25, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 129, 129, 74, 74, 70, 70, 1, 1] 129 rigid atoms, others: [7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 19, 20, 21, 22, 23, 24]) total number of confs: 358 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567737 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567737 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 1: /scratch/stefan/7901150/working/building/REAL300025567737/1.* 0: /scratch/stefan/7901150/working/building/REAL300025567737/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567737 Building REAL300025567738 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567738' /scratch/stefan/7901150/working/building/REAL300025567738 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567738 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567738/0 /scratch/stefan/7901150/working/building/REAL300025567738 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 252) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/252 `/scratch/stefan/7901150/working/3D/252' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(S(C)(=O)=O)=C(C)C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=C1) `REAL300025567738.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567738.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567738/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567738 none CC1=CC(S(C)(=O)=O)=C(C)C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 1, 1, 1, 14, 5, 11, 11, 1, 5, 1, 14, 11, 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, 3, 3, 7, 7, 7, 7, 6, 6, 4, 7, 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 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 3, 3, 3, 3, 7, 7, 9, 9, 9, 9, 9, 1, 2, 2, 2, 1, 5, 5, 5, 2, 2, 2, 3, 7, 7, 7, 7, 1] 9 rigid atoms, others: [0, 1, 2, 3, 4, 39, 8, 9, 10, 11, 23, 27] set([5, 6, 7, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 59 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567738 none CC1=CC(S(C)(=O)=O)=C(C)C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 1, 1, 1, 14, 5, 11, 11, 1, 5, 1, 14, 11, 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, 3, 3, 7, 7, 7, 7, 6, 6, 4, 7, 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 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 6, 9] 9 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: 37 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567738 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567738 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567738/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567738 Building REAL300025567739 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567739' /scratch/stefan/7901150/working/building/REAL300025567739 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567739 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567739/0 /scratch/stefan/7901150/working/building/REAL300025567739 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 253) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/253 `/scratch/stefan/7901150/working/3D/253' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C(C(F)(F)F)C=C1S(=O)(=O)NCCC1=NC(=O)O[N-]1) `REAL300025567739.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567739.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567739/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567739 none COC(=O)C1=CC=C(C(F)(F)F)C=C1S(=O)(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.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, 11, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 14, 11, 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, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 1, 7, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 5, 5, 5, 11, 43, 68, 142, 142, 142, 142, 142, 7, 7, 7, 1, 1, 1, 11, 45, 45, 68, 68] 201 rigid atoms, others: [2, 4, 5, 6, 7, 8, 12, 13, 14, 29, 30, 31] set([0, 1, 3, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36]) total number of confs: 450 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567739 none COC(=O)C1=CC=C(C(F)(F)F)C=C1S(=O)(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.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, 11, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 14, 11, 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, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 142, 201, 142, 142, 142, 142, 142, 142, 142, 142, 142, 115, 77, 115, 115, 22, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 142, 142, 142, 77, 22, 22, 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]) total number of confs: 727 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567739 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567739 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567739/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567739 Building REAL300025567740 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567740' /scratch/stefan/7901150/working/building/REAL300025567740 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567740 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567740/0 /scratch/stefan/7901150/working/building/REAL300025567740 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 254) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/254 `/scratch/stefan/7901150/working/3D/254' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2=CC=C(OC3=CC=CC(Cl)=C3)C=C2)[N-]O1) `REAL300025567740.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567740.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567740/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567740 none O=C1N=C(CCNS(=O)(=O)C2=CC=C(OC3=CC=CC(Cl)=C3)C=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 16, 1, 1, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 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] 0 hydrogens need rotated 201 conformations in 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, 16, 43, 54, 54, 54, 54, 54, 54, 54, 150, 201, 201, 201, 201, 201, 201, 54, 54, 1, 1, 9, 9, 16, 16, 43, 54, 54, 201, 201, 201, 201, 54, 54] 201 rigid atoms, others: [0, 1, 2, 3, 4, 24, 25] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 436 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567740 none O=C1N=C(CCNS(=O)(=O)C2=CC=C(OC3=CC=CC(Cl)=C3)C=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 16, 1, 1, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 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] 0 hydrogens 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, 19, 13, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 8, 18, 18, 18, 18, 18, 18, 1, 1, 54, 54, 19, 19, 13, 13, 5, 1, 1, 18, 18, 18, 18, 1, 1] 201 rigid atoms, others: [32, 37, 38, 7, 10, 11, 12, 13, 14, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36]) total number of confs: 163 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567740 none O=C1N=C(CCNS(=O)(=O)C2=CC=C(OC3=CC=CC(Cl)=C3)C=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 16, 1, 1, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 98, 73, 33, 18, 18, 18, 18, 18, 18, 18, 8, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 201, 201, 98, 98, 73, 73, 33, 18, 18, 1, 1, 1, 1, 18, 18] 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: 594 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567740 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567740 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567740/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567740 Building REAL300025567741 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567741' /scratch/stefan/7901150/working/building/REAL300025567741 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567741 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567741/0 /scratch/stefan/7901150/working/building/REAL300025567741 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 255) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/255 `/scratch/stefan/7901150/working/3D/255' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=C1C) `REAL300025567741.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567741.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567741/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567741 none COC(=O)C1=CC=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.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.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'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 6, 6, 4, 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: [10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 21, 31, 112, 112, 112, 112, 112, 1, 1, 10, 10, 10, 1, 1, 1, 5, 21, 21, 31, 31, 2, 2, 2] 201 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 21, 22, 26, 27, 28] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 29, 30, 31, 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 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567741 none COC(=O)C1=CC=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.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.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'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 6, 6, 4, 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, 112, 201, 112, 112, 112, 112, 112, 79, 112, 112, 24, 8, 1, 1, 1, 1, 1, 1, 1, 112, 112, 201, 201, 201, 112, 112, 112, 79, 24, 24, 8, 8, 112, 112, 112] 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: 727 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567741 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567741 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567741/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567741 Building REAL300025567742 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567742' /scratch/stefan/7901150/working/building/REAL300025567742 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567742 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567742/0 /scratch/stefan/7901150/working/building/REAL300025567742 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 256) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/256 `/scratch/stefan/7901150/working/3D/256' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(Cl)C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=C1) `REAL300025567742.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567742.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567742/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567742 none COC1=CC=C(Cl)C(S(=O)(=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', 'Cl', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 16, 1, 14, 11, 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, 7, 7, 7, 6, 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, 5, 5, 5, 9, 34, 60, 199, 199, 199, 199, 199, 1, 3, 3, 3, 1, 1, 9, 34, 34, 60, 60, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 20, 24, 25, 31] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 26, 27, 28, 29, 30]) total number of confs: 444 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567742 none COC1=CC=C(Cl)C(S(=O)(=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', 'Cl', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 16, 1, 14, 11, 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, 7, 7, 7, 6, 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, 199, 199, 199, 199, 199, 199, 195, 108, 195, 195, 24, 8, 1, 1, 1, 1, 1, 1, 1, 199, 201, 201, 201, 199, 199, 108, 24, 24, 8, 8, 199] 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: 781 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567742 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567742 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567742/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567742 Building REAL300025567743 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567743' /scratch/stefan/7901150/working/building/REAL300025567743 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567743 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567743/0 /scratch/stefan/7901150/working/building/REAL300025567743 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 257) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/257 `/scratch/stefan/7901150/working/3D/257' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=CN=C1Cl) `REAL300025567743.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567743.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567743/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567743 none CC1=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=CN=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 1, 16, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 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: [1, 1, 1, 1, 1, 3, 3, 3, 9, 51, 92, 201, 201, 201, 201, 201, 1, 1, 1, 1, 2, 2, 2, 1, 9, 51, 51, 92, 92, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 16, 17, 18, 19, 23, 29] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 24, 25, 26, 27, 28]) total number of confs: 578 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567743 none CC1=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=CN=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 1, 16, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 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, 201, 201, 119, 82, 119, 119, 24, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 82, 24, 24, 8, 8, 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]) total number of confs: 635 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567743 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567743 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567743/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567743 Building REAL300025567744 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567744' /scratch/stefan/7901150/working/building/REAL300025567744 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567744 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567744/0 /scratch/stefan/7901150/working/building/REAL300025567744 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 258) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/258 `/scratch/stefan/7901150/working/3D/258' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=C(C)NN=C1S(=O)(=O)NCCC1=NC(=O)O[N-]1) `REAL300025567744.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567744.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567744/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567744 none COC(=O)C1=C(C)NN=C1S(=O)(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', '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, 11, 1, 1, 5, 8, 8, 1, 14, 11, 11, 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: [7, 3, 7, 5, 7, 7, 7, 4, 7, 7, 7, 6, 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 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 5, 6, 6, 9, 9, 9, 9, 9, 2, 2, 2, 2, 2, 2, 1, 5, 6, 6, 6, 6] 9 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 28] set([0, 1, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33]) total number of confs: 39 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567744 none COC(=O)C1=C(C)NN=C1S(=O)(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', '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, 11, 1, 1, 5, 8, 8, 1, 14, 11, 11, 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: [7, 3, 7, 5, 7, 7, 7, 4, 7, 7, 7, 6, 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 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 7, 9, 9, 6, 5, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 7, 6, 6, 5, 5] 9 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: 38 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567744 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567744 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567744/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567744 Building REAL300025567745 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567745' /scratch/stefan/7901150/working/building/REAL300025567745 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567745 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567745/0 /scratch/stefan/7901150/working/building/REAL300025567745 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 259) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/259 `/scratch/stefan/7901150/working/3D/259' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C(C)=C1C) `REAL300025567745.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567745.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567745/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567745 none COC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C(C)=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.3', '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, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 5, 1, 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, 6, 4, 7, 7, 7, 7, 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, 1, 1, 1, 1, 1, 1, 5, 5, 5, 9, 42, 71, 199, 199, 199, 199, 199, 1, 1, 1, 1, 4, 4, 4, 1, 1, 9, 42, 42, 71, 71, 2, 2, 2, 2, 2, 2] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 18, 19, 20, 21, 25, 26] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 513 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567745 none COC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C(C)=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.3', '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, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 5, 1, 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, 6, 4, 7, 7, 7, 7, 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, 199, 199, 199, 199, 187, 102, 187, 187, 24, 8, 1, 1, 1, 1, 1, 1, 1, 199, 199, 199, 199, 201, 201, 201, 199, 199, 102, 24, 24, 8, 8, 199, 199, 199, 199, 199, 199] 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: 762 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567745 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567745 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567745/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567745 Building REAL300025567746 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567746' /scratch/stefan/7901150/working/building/REAL300025567746 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567746 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567746/0 /scratch/stefan/7901150/working/building/REAL300025567746 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 260) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/260 `/scratch/stefan/7901150/working/3D/260' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2=CC(Br)=CC([N+](=O)[O-])=C2)[N-]O1) `REAL300025567746.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567746.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567746/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567746 none O=C1N=C(CCNS(=O)(=O)C2=CC(Br)=CC([N+](=O)[O-])=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 17, 1, 1, 8, 11, 11, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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: [1, 1, 1, 1, 1, 9, 25, 94, 127, 127, 127, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 9, 9, 25, 25, 94, 201, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 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]) total number of confs: 614 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567746 none O=C1N=C(CCNS(=O)(=O)C2=CC(Br)=CC([N+](=O)[O-])=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 17, 1, 1, 8, 11, 11, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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: [201, 201, 201, 83, 49, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 201, 201, 83, 83, 49, 49, 9, 1, 1, 1] 201 rigid atoms, others: [7, 10, 11, 12, 13, 14, 15, 16, 19, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 17, 18, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 543 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567746 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567746 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567746/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567746 Building REAL300025567747 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567747' /scratch/stefan/7901150/working/building/REAL300025567747 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567747 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567747/0 /scratch/stefan/7901150/working/building/REAL300025567747 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 261) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/261 `/scratch/stefan/7901150/working/3D/261' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1) `REAL300025567747.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567747/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567747 none COC(=O)CC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.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, 5, 1, 1, 1, 1, 14, 11, 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, 6, 4, 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 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [15, 15, 3, 15, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 24, 24, 24, 24, 24, 1, 1, 15, 15, 15, 3, 3, 1, 1, 8, 8, 8, 8, 8, 1, 1] 57 rigid atoms, others: [35, 4, 5, 6, 7, 8, 9, 21, 22, 36, 28, 29] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567747 none COC(=O)CC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.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, 5, 1, 1, 1, 1, 14, 11, 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, 6, 4, 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 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [57, 57, 29, 57, 19, 19, 24, 24, 19, 11, 19, 19, 11, 7, 1, 1, 1, 1, 1, 1, 1, 24, 24, 57, 57, 57, 29, 29, 24, 24, 11, 11, 11, 7, 7, 24, 24] 57 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: 269 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567747 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567747 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567747/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567747 Building REAL300025567748 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567748' /scratch/stefan/7901150/working/building/REAL300025567748 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567748 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567748/0 /scratch/stefan/7901150/working/building/REAL300025567748 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 262) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/262 `/scratch/stefan/7901150/working/3D/262' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1C(=O)N(C)C) `REAL300025567748.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567748.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567748/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567748 none COC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1C(=O)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 2, 2, 2, 9, 39, 65, 151, 151, 151, 151, 151, 1, 1, 1, 5, 5, 5, 5, 4, 4, 4, 1, 1, 9, 39, 39, 65, 65, 1, 5, 5, 5, 5, 5, 5] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 18, 19, 20, 28, 29, 35] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41]) total number of confs: 446 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567748 none COC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1C(=O)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 151, 151, 151, 151, 120, 86, 120, 120, 24, 8, 1, 1, 1, 1, 1, 1, 1, 151, 151, 151, 201, 201, 201, 201, 197, 197, 197, 151, 151, 86, 24, 24, 8, 8, 151, 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, 41]) total number of confs: 805 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567748 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567748 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567748/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567748 Building REAL300025567749 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567749' /scratch/stefan/7901150/working/building/REAL300025567749 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567749 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567749/0 /scratch/stefan/7901150/working/building/REAL300025567749 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 263) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/263 `/scratch/stefan/7901150/working/3D/263' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCC2=CC=C(S(=O)(=O)NCCC3=NC(=O)O[N-]3)C=C21) `REAL300025567749.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567749.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567749/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567749 none CC(=O)N1CCC2=CC=C(S(=O)(=O)NCCC3=NC(=O)O[N-]3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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: [5, 1, 11, 8, 5, 5, 1, 1, 1, 1, 14, 11, 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] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 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, 3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 53, 89, 201, 201, 201, 201, 201, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 1, 9, 53, 53, 89, 89, 1] 201 rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 9, 10, 38, 22, 23, 27, 28, 29, 30, 31] set([0, 33, 2, 34, 36, 37, 35, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26]) total number of confs: 572 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567749 none CC(=O)N1CCC2=CC=C(S(=O)(=O)NCCC3=NC(=O)O[N-]3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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: [5, 1, 11, 8, 5, 5, 1, 1, 1, 1, 14, 11, 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] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 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, 201, 201, 201, 137, 89, 137, 137, 24, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 89, 24, 24, 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]) total number of confs: 655 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567749 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567749 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567749/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567749 Building REAL300025567750 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567750' /scratch/stefan/7901150/working/building/REAL300025567750 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025567750 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567750/0 /scratch/stefan/7901150/working/building/REAL300025567750 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 264) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/264 `/scratch/stefan/7901150/working/3D/264' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2=CC=CN=C2[N+](=O)[O-])[N-]O1) `REAL300025567750.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567750/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567750 none O=C1N=C(CCNS(=O)(=O)C2=CC=CN=C2[N+](=O)[O-])[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 8, 11, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 3, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 109 conformations in input total number of sets (complete confs): 109 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 9, 25, 81, 109, 109, 109, 109, 109, 109, 109, 109, 109, 109, 109, 1, 1, 9, 9, 25, 25, 81, 109, 109, 109] 109 rigid atoms, others: [0, 1, 2, 3, 4, 19, 20] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 424 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567750 none O=C1N=C(CCNS(=O)(=O)C2=CC=CN=C2[N+](=O)[O-])[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 8, 11, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 3, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 109 conformations in input total number of sets (complete confs): 109 using faster count positions algorithm for large data unique positions, atoms: [109, 109, 109, 53, 29, 5, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 109, 109, 53, 53, 29, 29, 5, 1, 1, 1] 109 rigid atoms, others: [7, 10, 11, 12, 13, 14, 15, 16, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 330 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567750 /scratch/stefan/7901150/working /scratch/stefan/7901150 mkdir: created directory `1' /scratch/stefan/7901150/working/building/REAL300025567750/1 /scratch/stefan/7901150/working/building/REAL300025567750 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 1 (index: 265) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/265 `/scratch/stefan/7901150/working/3D/265' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CC[N-]S(=O)(=O)C2=CC=CN=C2[N+](=O)[O-])[N-]O1) `REAL300025567750.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025567750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567750/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567750 none O=C1N=C(CC[N-]S(=O)(=O)C2=CC=CN=C2[N+](=O)[O-])[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 8, 11, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 3, 7, 7, 3, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 9, 9, 29, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 1, 1, 9, 9, 9, 9, 41, 41, 41] 41 rigid atoms, others: [0, 1, 2, 3, 4, 19, 20] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567750 none O=C1N=C(CC[N-]S(=O)(=O)C2=CC=CN=C2[N+](=O)[O-])[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 8, 11, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 3, 7, 7, 3, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [41, 41, 41, 19, 19, 5, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 41, 41, 19, 19, 19, 19, 1, 1, 1] 41 rigid atoms, others: [7, 10, 11, 12, 13, 14, 15, 16, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 108 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567750 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567750 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 1: /scratch/stefan/7901150/working/building/REAL300025567750/1.* 0: /scratch/stefan/7901150/working/building/REAL300025567750/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567750 Building REAL300025567751 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567751' /scratch/stefan/7901150/working/building/REAL300025567751 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567751 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567751/0 /scratch/stefan/7901150/working/building/REAL300025567751 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 266) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/266 `/scratch/stefan/7901150/working/3D/266' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2=CC([N+](=O)[O-])=CC=C2Br)[N-]O1) `REAL300025567751.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567751.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567751/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567751 none O=C1N=C(CCNS(=O)(=O)C2=CC([N+](=O)[O-])=CC=C2Br)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 8, 11, 11, 1, 1, 1, 17, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 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, 9, 25, 85, 108, 108, 108, 108, 108, 108, 108, 108, 108, 108, 108, 108, 1, 1, 9, 9, 25, 25, 85, 108, 108, 108] 108 rigid atoms, others: [0, 1, 2, 3, 4, 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]) total number of confs: 396 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567751 none O=C1N=C(CCNS(=O)(=O)C2=CC([N+](=O)[O-])=CC=C2Br)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 8, 11, 11, 1, 1, 1, 17, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 108 conformations in input total number of sets (complete confs): 108 using faster count positions algorithm for large data unique positions, atoms: [108, 108, 108, 47, 31, 5, 3, 1, 3, 3, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 108, 108, 47, 47, 31, 31, 5, 1, 1, 1] 108 rigid atoms, others: [7, 10, 11, 12, 13, 16, 17, 18, 19, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 14, 15, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 297 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567751 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567751 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567751/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567751 Building REAL300025567752 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567752' /scratch/stefan/7901150/working/building/REAL300025567752 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567752 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567752/0 /scratch/stefan/7901150/working/building/REAL300025567752 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 267) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/267 `/scratch/stefan/7901150/working/3D/267' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C(C)C)C(C)=C1S(=O)(=O)NCCC1=NC(=O)O[N-]1) `REAL300025567752.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567752.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567752/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567752 none CC1=NN(C(C)C)C(C)=C1S(=O)(=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', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', '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, 8, 5, 5, 5, 1, 5, 1, 14, 11, 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, 6, 6, 4, 7, 7, 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, 3, 3, 1, 1, 1, 1, 8, 8, 8, 14, 52, 83, 201, 201, 201, 201, 201, 2, 2, 2, 3, 4, 4, 4, 4, 4, 4, 2, 2, 2, 14, 52, 52, 83, 83] 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]) total number of confs: 578 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567752 none CC1=NN(C(C)C)C(C)=C1S(=O)(=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', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', '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, 8, 5, 5, 5, 1, 5, 1, 14, 11, 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, 6, 6, 4, 7, 7, 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, 165, 95, 165, 165, 24, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 95, 24, 25, 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: 696 number of broken/clashed sets: 9 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567752 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567752 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567752/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567752 Building REAL300025567753 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567753' /scratch/stefan/7901150/working/building/REAL300025567753 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567753 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567753/0 /scratch/stefan/7901150/working/building/REAL300025567753 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 268) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/268 `/scratch/stefan/7901150/working/3D/268' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)CC2=CC=CC3=CC=CN=C32)[N-]O1) `REAL300025567753.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567753.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567753/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567753 none O=C1N=C(CCNS(=O)(=O)CC2=CC=CC3=CC=CN=C32)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in 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, 20, 69, 113, 113, 113, 167, 201, 201, 201, 201, 201, 201, 199, 201, 201, 1, 1, 8, 8, 20, 20, 69, 167, 167, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 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, 35]) total number of confs: 807 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567753 none O=C1N=C(CCNS(=O)(=O)CC2=CC=CC3=CC=CN=C32)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 123, 103, 35, 14, 2, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 123, 123, 103, 103, 35, 2, 2, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 671 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567753 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567753 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567753/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567753 Building REAL300025567754 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567754' /scratch/stefan/7901150/working/building/REAL300025567754 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567754 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567754/0 /scratch/stefan/7901150/working/building/REAL300025567754 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 269) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/269 `/scratch/stefan/7901150/working/3D/269' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(Cl)=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=C1) `REAL300025567754.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567754.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567754/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567754 none COC(=O)C1=CC(Cl)=CC(S(=O)(=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', 'Cl', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 16, 1, 1, 14, 11, 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, 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, 1, 9, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 45, 62, 128, 128, 128, 128, 128, 1, 9, 9, 9, 1, 1, 9, 45, 45, 62, 62, 1] 201 rigid atoms, others: [33, 2, 4, 5, 6, 7, 8, 9, 10, 22, 26, 27] set([0, 1, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 28, 29, 30, 31, 32]) total number of confs: 387 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567754 none COC(=O)C1=CC(Cl)=CC(S(=O)(=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', 'Cl', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 16, 1, 1, 14, 11, 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, 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, 128, 201, 128, 128, 128, 128, 128, 78, 55, 78, 78, 22, 8, 1, 1, 1, 1, 1, 1, 1, 128, 201, 201, 201, 128, 128, 55, 22, 22, 8, 8, 128] 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: 713 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567754 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567754 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567754/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567754 Building REAL300025567755 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567755' /scratch/stefan/7901150/working/building/REAL300025567755 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567755 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567755/0 /scratch/stefan/7901150/working/building/REAL300025567755 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 270) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/270 `/scratch/stefan/7901150/working/3D/270' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1N=C(C)C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=C1C) `REAL300025567755.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567755.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567755/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567755 none CCN1N=C(C)C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 5, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 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: [6, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 11, 38, 50, 122, 122, 122, 122, 122, 1, 1, 6, 6, 6, 6, 6, 2, 2, 2, 11, 38, 38, 50, 50, 2, 2, 2] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 19, 20] set([0, 8, 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, 36]) total number of confs: 361 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567755 none CCN1N=C(C)C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 5, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 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, 122, 122, 122, 122, 122, 90, 61, 90, 90, 23, 8, 1, 1, 1, 1, 1, 1, 1, 122, 122, 201, 201, 201, 201, 201, 122, 122, 122, 61, 23, 24, 8, 8, 122, 122, 122] 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: 889 number of broken/clashed sets: 15 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567755 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567755 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567755/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567755 Building REAL300025567756 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567756' /scratch/stefan/7901150/working/building/REAL300025567756 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567756 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567756/0 /scratch/stefan/7901150/working/building/REAL300025567756 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 271) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/271 `/scratch/stefan/7901150/working/3D/271' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1C) `REAL300025567756.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567756.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567756/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567756 none COC(=O)C1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.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'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 5, 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, 7, 6, 6, 4, 7, 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, 9, 1, 9, 1, 1, 1, 1, 1, 3, 3, 3, 9, 27, 39, 98, 98, 98, 98, 98, 1, 1, 1, 9, 9, 9, 1, 1, 9, 27, 27, 39, 39, 1, 2, 2, 2] 201 rigid atoms, others: [33, 2, 4, 5, 6, 7, 8, 20, 21, 22, 26, 27] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 28, 29, 30, 31, 32, 34, 35, 36]) total number of confs: 287 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567756 none COC(=O)C1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.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'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 5, 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, 7, 6, 6, 4, 7, 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, 98, 201, 98, 98, 98, 58, 46, 58, 58, 14, 8, 1, 1, 1, 1, 1, 1, 1, 98, 98, 98, 201, 201, 201, 98, 98, 46, 14, 14, 8, 8, 98, 98, 98, 98] 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: 637 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567756 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567756 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567756/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567756 Building REAL300025567757 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567757' /scratch/stefan/7901150/working/building/REAL300025567757 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567757 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567757/0 /scratch/stefan/7901150/working/building/REAL300025567757 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 272) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/272 `/scratch/stefan/7901150/working/3D/272' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC1=CC(F)=C(S(=O)(=O)[N-]CCC2=NC(=O)O[N-]2)C(F)=C1Cl) `REAL300025567757.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567757.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567757/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567757 none CC(=O)NC1=CC(F)=C(S(=O)(=O)[N-]CCC2=NC(=O)O[N-]2)C(F)=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'F', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 15, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 15, 1, 16, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 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, 13, 13, 13, 27, 68, 71, 158, 158, 158, 158, 158, 1, 1, 1, 1, 4, 4, 4, 4, 1, 68, 68, 71, 71] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 21, 22, 23, 24, 29] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 30, 31, 32, 33]) total number of confs: 405 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567757 none CC(=O)NC1=CC(F)=C(S(=O)(=O)[N-]CCC2=NC(=O)O[N-]2)C(F)=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'F', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 15, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 15, 1, 16, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 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, 158, 89, 158, 158, 158, 43, 25, 43, 43, 10, 8, 1, 1, 1, 1, 1, 1, 1, 158, 158, 158, 158, 201, 201, 201, 201, 158, 11, 11, 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: 764 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567757 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567757 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567757/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567757 Building REAL300025567758 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567758' /scratch/stefan/7901150/working/building/REAL300025567758 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567758 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567758/0 /scratch/stefan/7901150/working/building/REAL300025567758 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 273) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/273 `/scratch/stefan/7901150/working/3D/273' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=CC=C1[N+](=O)[O-]) `REAL300025567758.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567758/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567758 none CC1=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=CC=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [5, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 8, 11, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in 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, 9, 54, 93, 201, 201, 201, 201, 201, 1, 1, 1, 1, 2, 2, 2, 2, 2, 1, 9, 54, 54, 93, 93, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 32, 16, 17, 18, 19, 25, 31] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30]) total number of confs: 581 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567758 none CC1=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=CC=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [5, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 8, 11, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 113, 79, 113, 113, 24, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 79, 24, 24, 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]) total number of confs: 611 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567758 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567758 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567758/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567758 Building REAL300025567759 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567759' /scratch/stefan/7901150/working/building/REAL300025567759 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567759 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567759/0 /scratch/stefan/7901150/working/building/REAL300025567759 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 274) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/274 `/scratch/stefan/7901150/working/3D/274' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CCN(C)S(=O)(=O)NCCC1=NC(=O)O[N-]1) `REAL300025567759.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567759.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567759/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567759 none COC(=O)CCN(C)S(=O)(=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', 'N.pl3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', '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, 12, 1, 11, 5, 5, 8, 5, 14, 11, 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, 3, 7, 5, 7, 7, 7, 7, 7, 6, 6, 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, 115, 201, 115, 92, 60, 92, 43, 60, 60, 8, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 115, 115, 115, 115, 92, 92, 92, 43, 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, 30, 31, 32, 33, 34]) total number of confs: 739 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567759 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567759 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567759/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567759 Building REAL300025567760 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567760' /scratch/stefan/7901150/working/building/REAL300025567760 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567760 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567760/0 /scratch/stefan/7901150/working/building/REAL300025567760 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 275) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/275 `/scratch/stefan/7901150/working/3D/275' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN1C=NC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=C1) `REAL300025567760.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567760.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567760/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567760 none CC(C)CN1C=NC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 5, 5, 8, 1, 8, 1, 14, 11, 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, 6, 6, 4, 7, 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, 7, 1, 1, 1, 1, 1, 1, 6, 6, 6, 18, 56, 59, 139, 139, 139, 139, 139, 1, 7, 7, 7, 7, 7, 7, 7, 4, 4, 1, 18, 56, 56, 59, 59, 1] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 20, 36, 30] set([0, 1, 2, 9, 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: 385 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567760 none CC(C)CN1C=NC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 5, 5, 8, 1, 8, 1, 14, 11, 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, 6, 6, 4, 7, 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, 200, 201, 139, 139, 139, 139, 89, 62, 89, 89, 17, 8, 1, 1, 1, 1, 1, 1, 1, 139, 201, 201, 201, 201, 201, 201, 201, 200, 200, 139, 62, 17, 17, 8, 8, 139] 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: 792 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567760 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567760 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567760/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567760 Building REAL300025567761 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567761' /scratch/stefan/7901150/working/building/REAL300025567761 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567761 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567761/0 /scratch/stefan/7901150/working/building/REAL300025567761 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 276) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/276 `/scratch/stefan/7901150/working/3D/276' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=C(F)C=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=C1F) `REAL300025567761.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567761/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567761 none COC(=O)C1=C(F)C=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 15, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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: [13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 21, 50, 52, 137, 137, 137, 137, 137, 1, 1, 13, 13, 13, 1, 1, 21, 50, 50, 52, 52] 201 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 22, 23, 27, 28] set([0, 1, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 29, 30, 31, 32, 33]) total number of confs: 362 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567761 none COC(=O)C1=C(F)C=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 15, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 137, 201, 137, 137, 137, 137, 135, 78, 53, 78, 78, 18, 8, 1, 1, 1, 1, 1, 1, 1, 137, 137, 201, 201, 201, 137, 137, 53, 18, 18, 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: 668 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567761 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567761 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567761/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567761 Building REAL300025567762 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567762' /scratch/stefan/7901150/working/building/REAL300025567762 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567762 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567762/0 /scratch/stefan/7901150/working/building/REAL300025567762 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 277) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/277 `/scratch/stefan/7901150/working/3D/277' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)CCCS(=O)(=O)NCCC1=NC(=O)O[N-]1) `REAL300025567762.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567762/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567762 none CS(=O)(=O)CCCS(=O)(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', '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, 5, 5, 5, 14, 11, 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, 6, 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 56 conformations in input total number of sets (complete confs): 56 using faster count positions algorithm for large data unique positions, atoms: [56, 34, 56, 56, 34, 26, 23, 17, 23, 23, 11, 7, 1, 1, 1, 1, 1, 1, 1, 56, 56, 56, 34, 34, 34, 34, 26, 26, 17, 11, 11, 7, 7] 56 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: 273 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567762 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567762 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567762/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567762 Building REAL300025567763 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567763' /scratch/stefan/7901150/working/building/REAL300025567763 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567763 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567763/0 /scratch/stefan/7901150/working/building/REAL300025567763 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 278) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/278 `/scratch/stefan/7901150/working/3D/278' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2=CC=C3CCNC(=O)C3=C2)[N-]O1) `REAL300025567763.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567763.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567763/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567763 none O=C1N=C(CCNS(=O)(=O)C2=CC=C3CCNC(=O)C3=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 5, 5, 8, 1, 11, 1, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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, 9, 25, 92, 143, 143, 143, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 9, 9, 25, 25, 92, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 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, 35]) total number of confs: 677 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567763 none O=C1N=C(CCNS(=O)(=O)C2=CC=C3CCNC(=O)C3=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 5, 5, 8, 1, 11, 1, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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, 88, 53, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 88, 88, 53, 53, 9, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 547 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567763 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567763 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567763/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567763 Building REAL300025567764 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567764' /scratch/stefan/7901150/working/building/REAL300025567764 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567764 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567764/0 /scratch/stefan/7901150/working/building/REAL300025567764 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 279) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/279 `/scratch/stefan/7901150/working/3D/279' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)CC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1) `REAL300025567764.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567764/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567764 none CS(=O)(=O)CC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.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, 14, 11, 11, 5, 1, 1, 1, 1, 14, 11, 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, 3, 7, 7, 7, 7, 7, 7, 6, 6, 4, 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 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [8, 2, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 1, 1, 8, 8, 8, 2, 2, 1, 1, 5, 5, 5, 5, 5, 1, 1] 15 rigid atoms, others: [35, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 36, 28, 29] set([0, 1, 2, 3, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34]) total number of confs: 42 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567764 none CS(=O)(=O)CC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.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, 14, 11, 11, 5, 1, 1, 1, 1, 14, 11, 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, 3, 7, 7, 7, 7, 7, 7, 6, 6, 4, 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 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [15, 7, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 5, 5, 7, 7] 15 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: 70 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567764 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567764 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567764/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567764 Building REAL300025567765 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567765' /scratch/stefan/7901150/working/building/REAL300025567765 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567765 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567765/0 /scratch/stefan/7901150/working/building/REAL300025567765 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 280) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/280 `/scratch/stefan/7901150/working/3D/280' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)N1CCC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)CC1) `REAL300025567765.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567765.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567765/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567765 none CCOC(=O)N1CCC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 5, 12, 1, 11, 8, 5, 5, 5, 14, 11, 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, 3, 7, 6, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 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: [15, 6, 2, 1, 2, 1, 1, 1, 1, 1, 6, 6, 6, 19, 38, 49, 123, 123, 123, 123, 123, 1, 1, 15, 15, 15, 14, 14, 1, 1, 1, 1, 1, 19, 38, 38, 49, 49, 1, 1, 1, 1] 201 rigid atoms, others: [32, 3, 5, 6, 7, 8, 9, 39, 40, 21, 22, 41, 38, 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, 33, 34, 35, 36, 37]) total number of confs: 372 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567765 none CCOC(=O)N1CCC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 5, 12, 1, 11, 8, 5, 5, 5, 14, 11, 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, 3, 7, 6, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 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, 180, 177, 123, 177, 123, 123, 123, 97, 61, 97, 97, 21, 8, 1, 1, 1, 1, 1, 1, 1, 123, 123, 201, 201, 201, 201, 201, 123, 123, 123, 123, 123, 61, 21, 21, 8, 8, 123, 123, 123, 123] 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: 833 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567765 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567765 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567765/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567765 Building REAL300025567766 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567766' /scratch/stefan/7901150/working/building/REAL300025567766 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567766 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567766/0 /scratch/stefan/7901150/working/building/REAL300025567766 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 281) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/281 `/scratch/stefan/7901150/working/3D/281' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=C(F)C=C(Br)C=C1S(=O)(=O)NCCC1=NC(=O)O[N-]1) `REAL300025567766.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567766.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567766/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567766 none COC1=C(F)C=C(Br)C=C1S(=O)(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', '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, 15, 1, 1, 17, 1, 1, 14, 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: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 17, 57, 81, 201, 201, 201, 201, 201, 3, 3, 3, 1, 1, 17, 57, 57, 81, 81] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 25, 26] set([0, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31]) total number of confs: 536 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567766 none COC1=C(F)C=C(Br)C=C1S(=O)(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', '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, 15, 1, 1, 17, 1, 1, 14, 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: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 193, 201, 201, 201, 157, 86, 157, 157, 22, 9, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 86, 22, 22, 9, 9] 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: 741 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567766 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567766 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567766/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567766 Building REAL300025567767 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567767' /scratch/stefan/7901150/working/building/REAL300025567767 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567767 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567767/0 /scratch/stefan/7901150/working/building/REAL300025567767 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 282) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/282 `/scratch/stefan/7901150/working/3D/282' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=C(Cl)C=CC=C1S(=O)(=O)NCCC1=NC(=O)O[N-]1) `REAL300025567767.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567767.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567767/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567767 none N#CC1=C(Cl)C=CC=C1S(=O)(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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: [8, 1, 1, 1, 16, 1, 1, 1, 1, 14, 11, 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, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 5, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 13, 63, 95, 201, 201, 201, 201, 201, 1, 1, 1, 13, 65, 65, 95, 95] 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]) total number of confs: 587 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567767 none N#CC1=C(Cl)C=CC=C1S(=O)(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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: [8, 1, 1, 1, 16, 1, 1, 1, 1, 14, 11, 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, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 5, 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: [201, 201, 201, 201, 201, 201, 201, 201, 168, 103, 168, 168, 24, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 103, 25, 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]) total number of confs: 701 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567767 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567767 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567767/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567767 Building REAL300025567768 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567768' /scratch/stefan/7901150/working/building/REAL300025567768 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567768 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567768/0 /scratch/stefan/7901150/working/building/REAL300025567768 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 283) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/283 `/scratch/stefan/7901150/working/3D/283' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C#N)C=C1S(=O)(=O)NCCC1=NC(=O)O[N-]1) `REAL300025567768.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567768.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567768/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567768 none CC1=CC=C(C#N)C=C1S(=O)(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.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, 1, 1, 8, 1, 1, 14, 11, 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, 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 182 conformations in input total number of sets (complete confs): 182 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 48, 89, 182, 182, 182, 182, 182, 2, 2, 2, 1, 1, 1, 12, 50, 50, 89, 89] 182 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]) total number of confs: 544 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567768 none CC1=CC=C(C#N)C=C1S(=O)(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.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, 1, 1, 8, 1, 1, 14, 11, 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, 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 182 conformations in input total number of sets (complete confs): 182 using faster count positions algorithm for large data unique positions, atoms: [182, 182, 182, 182, 182, 182, 182, 182, 177, 108, 177, 177, 24, 8, 1, 1, 1, 1, 1, 1, 1, 182, 182, 182, 182, 182, 182, 108, 24, 24, 8, 8] 182 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: 673 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567768 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567768 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567768/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567768 Building REAL300025567769 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567769' /scratch/stefan/7901150/working/building/REAL300025567769 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025567769 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567769/0 /scratch/stefan/7901150/working/building/REAL300025567769 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 284) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/284 `/scratch/stefan/7901150/working/3D/284' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2=CC=C(Cl)C(C3=N[N-]N=N3)=C2)[N-]O1) `REAL300025567769.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567769.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567769/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567769 none O=C1N=C(CCNS(=O)(=O)C2=CC=C(Cl)C(C3=N[N-]N=N3)=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 16, 1, 1, 8, 8, 8, 8, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 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 201 conformations in 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, 25, 94, 142, 142, 142, 168, 168, 168, 168, 168, 168, 201, 201, 201, 201, 168, 1, 1, 9, 9, 25, 25, 94, 168, 168, 168] 201 rigid atoms, others: [0, 1, 2, 3, 4, 22, 23] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 665 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567769 none O=C1N=C(CCNS(=O)(=O)C2=CC=C(Cl)C(C3=N[N-]N=N3)=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 16, 1, 1, 8, 8, 8, 8, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [168, 168, 168, 64, 50, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 1, 168, 168, 64, 64, 50, 50, 9, 1, 1, 1] 201 rigid atoms, others: [7, 10, 11, 12, 13, 14, 15, 16, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 415 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567769 none O=C1N=C(CCNS(=O)(=O)C2=CC=C(Cl)C(C3=N[N-]N=N3)=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 16, 1, 1, 8, 8, 8, 8, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 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 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 18, 18, 17, 9, 5, 9, 9, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 21, 21, 18, 18, 18, 18, 17, 5, 5, 5] 21 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 66 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567769 /scratch/stefan/7901150/working /scratch/stefan/7901150 mkdir: created directory `1' /scratch/stefan/7901150/working/building/REAL300025567769/1 /scratch/stefan/7901150/working/building/REAL300025567769 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 1 (index: 285) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/285 `/scratch/stefan/7901150/working/3D/285' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2=CC=C(Cl)C(C3=NN=N[N-]3)=C2)[N-]O1) `REAL300025567769.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025567769.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567769/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567769 none O=C1N=C(CCNS(=O)(=O)C2=CC=C(Cl)C(C3=NN=N[N-]3)=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 16, 1, 1, 8, 8, 8, 8, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 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 201 conformations in 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, 25, 90, 139, 139, 139, 165, 165, 165, 165, 165, 165, 201, 201, 201, 201, 165, 1, 1, 9, 9, 25, 25, 90, 165, 165, 165] 201 rigid atoms, others: [0, 1, 2, 3, 4, 22, 23] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 666 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567769 none O=C1N=C(CCNS(=O)(=O)C2=CC=C(Cl)C(C3=NN=N[N-]3)=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 16, 1, 1, 8, 8, 8, 8, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [165, 165, 165, 64, 50, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 1, 165, 165, 64, 64, 50, 50, 9, 1, 1, 1] 201 rigid atoms, others: [7, 10, 11, 12, 13, 14, 15, 16, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 413 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567769 none O=C1N=C(CCNS(=O)(=O)C2=CC=C(Cl)C(C3=NN=N[N-]3)=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 16, 1, 1, 8, 8, 8, 8, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 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 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, 20, 20, 20, 9, 5, 9, 9, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 22, 22, 20, 20, 20, 20, 20, 5, 5, 5] 22 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 70 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567769 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567769 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 1: /scratch/stefan/7901150/working/building/REAL300025567769/1.* 0: /scratch/stefan/7901150/working/building/REAL300025567769/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567769 Building REAL300025567770 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567770' /scratch/stefan/7901150/working/building/REAL300025567770 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567770 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567770/0 /scratch/stefan/7901150/working/building/REAL300025567770 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 286) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/286 `/scratch/stefan/7901150/working/3D/286' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC1=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=CC=C1F) `REAL300025567770.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567770.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567770/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567770 none CC(=O)NC1=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=CC=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 15, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 6, 6, 4, 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, 3, 1, 1, 1, 1, 1, 3, 3, 3, 9, 49, 78, 173, 173, 173, 173, 173, 1, 1, 1, 1, 3, 3, 3, 3, 1, 9, 49, 49, 78, 78, 1, 1] 201 rigid atoms, others: [33, 34, 3, 4, 5, 6, 7, 19, 20, 21, 22, 27] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 28, 29, 30, 31, 32]) total number of confs: 504 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567770 none CC(=O)NC1=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=CC=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 15, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 6, 6, 4, 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, 173, 173, 173, 114, 80, 114, 114, 24, 8, 1, 1, 1, 1, 1, 1, 1, 173, 173, 173, 173, 201, 201, 201, 201, 173, 80, 25, 25, 8, 8, 173, 173] 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]) total number of confs: 670 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567770 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567770 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567770/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567770 Building REAL300025567771 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567771' /scratch/stefan/7901150/working/building/REAL300025567771 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567771 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567771/0 /scratch/stefan/7901150/working/building/REAL300025567771 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 287) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/287 `/scratch/stefan/7901150/working/3D/287' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2=CC=C(OCC(F)F)C3=CC=CC=C32)[N-]O1) `REAL300025567771.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567771.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567771/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567771 none O=C1N=C(CCNS(=O)(=O)C2=CC=C(OCC(F)F)C3=CC=CC=C32)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', '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'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 5, 15, 15, 1, 1, 1, 1, 1, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 9, 19, 48, 63, 63, 63, 63, 63, 63, 63, 138, 201, 201, 201, 63, 63, 63, 63, 63, 63, 1, 1, 9, 9, 19, 19, 48, 63, 63, 201, 201, 201, 63, 63, 63, 63] 201 rigid atoms, others: [0, 1, 2, 3, 4, 25, 26] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 700 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567771 none O=C1N=C(CCNS(=O)(=O)C2=CC=C(OCC(F)F)C3=CC=CC=C32)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', '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'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 5, 15, 15, 1, 1, 1, 1, 1, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 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: [63, 63, 63, 19, 11, 3, 3, 1, 3, 3, 1, 1, 1, 1, 1, 7, 21, 41, 41, 1, 1, 1, 1, 1, 1, 63, 63, 19, 19, 11, 11, 3, 1, 1, 21, 21, 41, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 37, 38, 7, 40, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 24, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36]) total number of confs: 322 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567771 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567771 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567771/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567771 Building REAL300025567772 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567772' /scratch/stefan/7901150/working/building/REAL300025567772 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567772 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567772/0 /scratch/stefan/7901150/working/building/REAL300025567772 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 288) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/288 `/scratch/stefan/7901150/working/3D/288' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2=CC=C(Br)C=N2)[N-]O1) `REAL300025567772.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567772.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567772/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567772 none O=C1N=C(CCNS(=O)(=O)C2=CC=C(Br)C=N2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 17, 1, 8, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 3, 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: [1, 1, 1, 1, 1, 9, 25, 102, 152, 152, 152, 201, 201, 201, 201, 201, 201, 1, 1, 9, 9, 25, 25, 102, 201, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 17, 18] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 670 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567772 none O=C1N=C(CCNS(=O)(=O)C2=CC=C(Br)C=N2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 17, 1, 8, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 3, 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: [201, 201, 201, 92, 68, 25, 6, 1, 6, 6, 1, 1, 1, 1, 1, 1, 1, 201, 201, 92, 92, 68, 68, 25, 1, 1, 1] 201 rigid atoms, others: [7, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 17, 18, 19, 20, 21, 22, 23]) total number of confs: 567 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567772 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567772 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567772/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567772 Building REAL300025567773 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567773' /scratch/stefan/7901150/working/building/REAL300025567773 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567773 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567773/0 /scratch/stefan/7901150/working/building/REAL300025567773 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 289) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/289 `/scratch/stefan/7901150/working/3D/289' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C1=CC=CC=C1S(=O)(=O)NCCC1=NC(=O)O[N-]1) `REAL300025567773.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567773.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567773/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567773 none CC(C)(C)C1=CC=CC=C1S(=O)(=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', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', '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, 1, 1, 1, 1, 1, 1, 14, 11, 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, 6, 6, 4, 7, 7, 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 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 8, 15, 31, 31, 31, 31, 31, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 8, 8, 15, 15] 31 rigid atoms, others: [32, 1, 34, 4, 5, 6, 7, 8, 9, 10, 33, 31] set([0, 2, 3, 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: 95 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567773 none CC(C)(C)C1=CC=CC=C1S(=O)(=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', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', '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, 1, 1, 1, 1, 1, 1, 14, 11, 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, 6, 6, 4, 7, 7, 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 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 18, 9, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 18, 18, 9, 9] 31 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: 117 number of broken/clashed sets: 30 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567773 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567773 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567773/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567773 Building REAL300025567774 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567774' /scratch/stefan/7901150/working/building/REAL300025567774 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567774 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567774/0 /scratch/stefan/7901150/working/building/REAL300025567774 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 290) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/290 `/scratch/stefan/7901150/working/3D/290' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2CCC3=CC=CC=C3C2)[N-]O1) `REAL300025567774.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567774.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567774/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567774 none O=C1N=C(CCNS(=O)(=O)C2CCC3=CC=CC=C3C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', '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, 1, 5, 5, 8, 14, 11, 11, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 9, 25, 95, 157, 157, 157, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 9, 9, 25, 25, 95, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 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, 32, 33, 34, 35, 36, 37]) total number of confs: 757 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567774 none O=C1N=C(CCNS(=O)(=O)C2CCC3=CC=CC=C3C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', '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, 1, 5, 5, 8, 14, 11, 11, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 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, 116, 89, 35, 10, 1, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 116, 116, 89, 89, 35, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 640 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567774 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567774 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567774/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567774 Building REAL300025567775 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567775' /scratch/stefan/7901150/working/building/REAL300025567775 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567775 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567775/0 /scratch/stefan/7901150/working/building/REAL300025567775 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 291) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/291 `/scratch/stefan/7901150/working/3D/291' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC2=CC=C(S(=O)(=O)NCCC3=NC(=O)O[N-]3)C=C2O1) `REAL300025567775.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567775.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567775/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567775 none CC1=NC2=CC=C(S(=O)(=O)NCCC3=NC(=O)O[N-]3)C=C2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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: [1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 56, 94, 201, 201, 201, 201, 201, 1, 1, 1, 2, 2, 2, 1, 1, 9, 56, 56, 94, 94, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 32, 19, 20, 21, 25, 26] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 27, 28, 29, 30, 31]) total number of confs: 578 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567775 none CC1=NC2=CC=C(S(=O)(=O)NCCC3=NC(=O)O[N-]3)C=C2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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: [201, 201, 201, 201, 201, 201, 117, 84, 117, 117, 24, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 84, 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, 32]) total number of confs: 610 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567775 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567775 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567775/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567775 Building REAL300025567776 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567776' /scratch/stefan/7901150/working/building/REAL300025567776 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567776 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567776/0 /scratch/stefan/7901150/working/building/REAL300025567776 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 292) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/292 `/scratch/stefan/7901150/working/3D/292' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC2=CC(S(=O)(=O)NCCC3=NC(=O)O[N-]3)=CC(Cl)=C2O1) `REAL300025567776.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567776.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567776/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567776 none CC1CC2=CC(S(=O)(=O)NCCC3=NC(=O)O[N-]3)=CC(Cl)=C2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 16, 1, 12, 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, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 54, 90, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 9, 54, 54, 90, 90, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 18, 19, 20, 21, 22, 26, 27, 28, 29, 35] set([32, 33, 34, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 30, 31]) total number of confs: 556 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567776 none CC1CC2=CC(S(=O)(=O)NCCC3=NC(=O)O[N-]3)=CC(Cl)=C2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 16, 1, 12, 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, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 126, 87, 126, 126, 24, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 87, 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, 34, 35]) total number of confs: 643 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567776 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567776 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567776/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567776 Building REAL300025567777 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567777' /scratch/stefan/7901150/working/building/REAL300025567777 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567777 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567777/0 /scratch/stefan/7901150/working/building/REAL300025567777 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 293) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/293 `/scratch/stefan/7901150/working/3D/293' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC1=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=CC=C1C) `REAL300025567777.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567777.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567777/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567777 none CC(=O)NC1=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', '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, 11, 8, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 5, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 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, 3, 3, 1, 1, 1, 1, 1, 3, 3, 3, 9, 47, 77, 169, 169, 169, 169, 169, 1, 1, 1, 1, 3, 3, 3, 3, 1, 9, 47, 47, 77, 77, 1, 1, 2, 2, 2] 201 rigid atoms, others: [33, 34, 3, 4, 5, 6, 7, 19, 20, 21, 22, 27] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 28, 29, 30, 31, 32, 35, 36, 37]) total number of confs: 508 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567777 none CC(=O)NC1=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', '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, 11, 8, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 5, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 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, 169, 169, 169, 117, 77, 117, 117, 24, 8, 1, 1, 1, 1, 1, 1, 1, 169, 169, 169, 169, 201, 201, 201, 201, 169, 77, 25, 25, 8, 8, 169, 169, 169, 169, 169] 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: 701 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567777 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567777 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567777/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567777 Building REAL300025567778 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567778' /scratch/stefan/7901150/working/building/REAL300025567778 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567778 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567778/0 /scratch/stefan/7901150/working/building/REAL300025567778 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 294) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/294 `/scratch/stefan/7901150/working/3D/294' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCCC2=CC=C(S(=O)(=O)NCCC3=NC(=O)O[N-]3)C=C21) `REAL300025567778.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567778.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567778/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567778 none CC(=O)N1CCCC2=CC=C(S(=O)(=O)NCCC3=NC(=O)O[N-]3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 14, 11, 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] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 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, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 53, 90, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 9, 53, 53, 90, 90, 1] 201 rigid atoms, others: [32, 1, 34, 3, 4, 5, 6, 7, 8, 9, 10, 11, 35, 41, 23, 24, 33, 28, 29, 30, 31] set([0, 2, 36, 37, 38, 39, 40, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27]) total number of confs: 569 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567778 none CC(=O)N1CCCC2=CC=C(S(=O)(=O)NCCC3=NC(=O)O[N-]3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 14, 11, 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] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 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, 201, 150, 91, 150, 150, 24, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 91, 24, 24, 8, 8, 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: 697 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567778 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567778 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567778/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567778 Building REAL300025567779 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567779' /scratch/stefan/7901150/working/building/REAL300025567779 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025567779 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567779/0 /scratch/stefan/7901150/working/building/REAL300025567779 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 295) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/295 `/scratch/stefan/7901150/working/3D/295' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(F)=CC(F)=C1S(=O)(=O)NCCC1=NC(=O)O[N-]1) `REAL300025567779.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567779.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567779/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567779 none COC1=CC(F)=CC(F)=C1S(=O)(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', '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, 15, 1, 1, 15, 1, 14, 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: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 11, 11, 11, 26, 75, 97, 201, 201, 201, 201, 201, 3, 3, 3, 1, 1, 26, 75, 75, 97, 97] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 25, 26] set([0, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31]) total number of confs: 604 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567779 none COC1=CC(F)=CC(F)=C1S(=O)(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', '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, 15, 1, 1, 15, 1, 14, 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: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 179, 201, 201, 201, 201, 134, 78, 134, 134, 22, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 78, 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]) total number of confs: 759 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567779 /scratch/stefan/7901150/working /scratch/stefan/7901150 mkdir: created directory `1' /scratch/stefan/7901150/working/building/REAL300025567779/1 /scratch/stefan/7901150/working/building/REAL300025567779 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 1 (index: 296) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/296 `/scratch/stefan/7901150/working/3D/296' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(F)=CC(F)=C1S(=O)(=O)[N-]CCC1=NC(=O)O[N-]1) `REAL300025567779.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025567779.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567779/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567779 none COC1=CC(F)=CC(F)=C1S(=O)(=O)[N-]CCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.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, 12, 1, 1, 1, 15, 1, 1, 15, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 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: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 30, 77, 79, 182, 182, 182, 182, 182, 4, 4, 4, 1, 1, 77, 77, 79, 79] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 25, 26] set([0, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30]) total number of confs: 458 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567779 none COC1=CC(F)=CC(F)=C1S(=O)(=O)[N-]CCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.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, 12, 1, 1, 1, 15, 1, 1, 15, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 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, 182, 182, 182, 162, 182, 182, 182, 182, 99, 41, 99, 99, 11, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 182, 182, 11, 11, 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]) total number of confs: 609 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567779 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567779 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 1: /scratch/stefan/7901150/working/building/REAL300025567779/1.* 0: /scratch/stefan/7901150/working/building/REAL300025567779/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567779 Building REAL300025567780 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567780' /scratch/stefan/7901150/working/building/REAL300025567780 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567780 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567780/0 /scratch/stefan/7901150/working/building/REAL300025567780 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 297) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/297 `/scratch/stefan/7901150/working/3D/297' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2=CN=C(Cl)C(Cl)=C2)[N-]O1) `REAL300025567780.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567780.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567780/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567780 none O=C1N=C(CCNS(=O)(=O)C2=CN=C(Cl)C(Cl)=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 8, 1, 16, 1, 16, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 3, 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: [1, 1, 1, 1, 1, 9, 25, 87, 121, 121, 121, 201, 201, 201, 201, 201, 201, 201, 1, 1, 9, 9, 25, 25, 87, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 18, 19] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 628 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567780 none O=C1N=C(CCNS(=O)(=O)C2=CN=C(Cl)C(Cl)=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 8, 1, 16, 1, 16, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 3, 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: [201, 201, 201, 89, 49, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 89, 89, 49, 49, 9, 1, 1] 201 rigid atoms, others: [7, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 563 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567780 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567780 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567780/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567780 Building REAL300025567781 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567781' /scratch/stefan/7901150/working/building/REAL300025567781 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567781 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567781/0 /scratch/stefan/7901150/working/building/REAL300025567781 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 298) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/298 `/scratch/stefan/7901150/working/3D/298' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C#N)=CC=C1S(=O)(=O)NCCC1=NC(=O)O[N-]1) `REAL300025567781.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567781.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567781/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567781 none CC1=CC(C#N)=CC=C1S(=O)(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.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, 1, 8, 1, 1, 1, 14, 11, 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, 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 143 conformations in input total number of sets (complete confs): 143 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 13, 39, 63, 143, 143, 143, 143, 143, 2, 2, 2, 1, 1, 1, 13, 41, 41, 63, 63] 143 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]) total number of confs: 402 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567781 none CC1=CC(C#N)=CC=C1S(=O)(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.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, 1, 8, 1, 1, 1, 14, 11, 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, 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 143 conformations in input total number of sets (complete confs): 143 using faster count positions algorithm for large data unique positions, atoms: [143, 141, 143, 143, 143, 143, 143, 143, 133, 85, 133, 133, 24, 8, 1, 1, 1, 1, 1, 1, 1, 143, 143, 143, 143, 143, 143, 85, 24, 24, 8, 8] 143 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: 539 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567781 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567781 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567781/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567781 Building REAL300025567782 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567782' /scratch/stefan/7901150/working/building/REAL300025567782 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567782 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567782/0 /scratch/stefan/7901150/working/building/REAL300025567782 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 299) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/299 `/scratch/stefan/7901150/working/3D/299' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2=CC=C(N3CCOC3=O)C=C2)[N-]O1) `REAL300025567782.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567782.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567782/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567782 none O=C1N=C(CCNS(=O)(=O)C2=CC=C(N3CCOC3=O)C=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 5, 5, 12, 1, 11, 1, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 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, 9, 25, 73, 109, 109, 109, 109, 109, 109, 109, 201, 201, 201, 201, 201, 109, 109, 1, 1, 9, 9, 25, 25, 73, 109, 109, 201, 201, 201, 201, 109, 109] 201 rigid atoms, others: [0, 1, 2, 3, 4, 22, 23] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 579 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567782 none O=C1N=C(CCNS(=O)(=O)C2=CC=C(N3CCOC3=O)C=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 5, 5, 12, 1, 11, 1, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 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: [109, 109, 109, 42, 25, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 7, 1, 1, 109, 109, 42, 42, 25, 25, 5, 1, 1, 7, 7, 6, 6, 1, 1] 201 rigid atoms, others: [35, 36, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 29, 30] set([0, 1, 2, 3, 4, 5, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34]) total number of confs: 289 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567782 none O=C1N=C(CCNS(=O)(=O)C2=CC=C(N3CCOC3=O)C=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 5, 5, 12, 1, 11, 1, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 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, 95, 66, 17, 6, 6, 6, 6, 2, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 201, 201, 95, 95, 66, 66, 17, 7, 7, 1, 1, 1, 1, 7, 7] 201 rigid atoms, others: [32, 33, 34, 13, 14, 15, 16, 17, 18, 19, 31] 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, 35, 36]) total number of confs: 603 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567782 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567782 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567782/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567782 Building REAL300025567783 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567783' /scratch/stefan/7901150/working/building/REAL300025567783 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567783 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567783/0 /scratch/stefan/7901150/working/building/REAL300025567783 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 300) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/300 `/scratch/stefan/7901150/working/3D/300' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=CC=C1OC) `REAL300025567783.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567783.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567783/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567783 none COC(=O)C1=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=CC=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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', '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, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 6, 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: [10, 10, 1, 10, 1, 1, 1, 1, 2, 2, 2, 9, 27, 37, 85, 85, 85, 85, 85, 1, 1, 1, 1, 3, 11, 11, 11, 1, 9, 27, 27, 37, 37, 1, 1, 4, 4, 4] 201 rigid atoms, others: [33, 2, 4, 5, 6, 7, 34, 19, 20, 21, 22, 27] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 28, 29, 30, 31, 32, 35, 36, 37]) total number of confs: 278 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567783 none COC(=O)C1=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=CC=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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', '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, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 6, 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: [201, 201, 85, 201, 85, 85, 51, 37, 51, 51, 14, 8, 1, 1, 1, 1, 1, 1, 1, 85, 85, 85, 85, 136, 201, 201, 201, 85, 37, 14, 14, 8, 8, 85, 85, 136, 136, 136] 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: 735 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567783 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567783 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567783/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567783 Building REAL300025567784 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567784' /scratch/stefan/7901150/working/building/REAL300025567784 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567784 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567784/0 /scratch/stefan/7901150/working/building/REAL300025567784 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 301) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/301 `/scratch/stefan/7901150/working/3D/301' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C(F)=C1) `REAL300025567784.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567784/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567784 none N#CC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C(F)=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 15, 1, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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, 1, 1, 7, 7, 7, 23, 74, 107, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 23, 74, 74, 107, 107, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 18, 19, 20, 21, 22, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27]) total number of confs: 618 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567784 none N#CC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C(F)=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 15, 1, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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, 147, 96, 147, 147, 24, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 96, 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]) total number of confs: 661 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567784 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567784 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567784/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567784 Building REAL300025567785 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567785' /scratch/stefan/7901150/working/building/REAL300025567785 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567785 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567785/0 /scratch/stefan/7901150/working/building/REAL300025567785 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 302) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/302 `/scratch/stefan/7901150/working/3D/302' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2=CC=CC(I)=C2)[N-]O1) `REAL300025567785.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567785.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567785/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567785 none O=C1N=C(CCNS(=O)(=O)C2=CC=CC(I)=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 18, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 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: [1, 1, 1, 1, 1, 9, 25, 82, 121, 121, 121, 201, 201, 201, 201, 201, 201, 1, 1, 9, 9, 25, 25, 82, 201, 201, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 17, 18] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 646 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567785 none O=C1N=C(CCNS(=O)(=O)C2=CC=CC(I)=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 18, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 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: [201, 201, 201, 92, 51, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 201, 201, 92, 92, 51, 51, 9, 1, 1, 1, 1] 201 rigid atoms, others: [7, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 17, 18, 19, 20, 21, 22, 23]) total number of confs: 576 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567785 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567785 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567785/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567785 Building REAL300025567786 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567786' /scratch/stefan/7901150/working/building/REAL300025567786 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025567786 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567786/0 /scratch/stefan/7901150/working/building/REAL300025567786 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 303) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/303 `/scratch/stefan/7901150/working/3D/303' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2=C(Cl)C=CC=C2C(F)(F)F)[N-]O1) `REAL300025567786.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567786.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567786/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567786 none O=C1N=C(CCNS(=O)(=O)C2=C(Cl)C=CC=C2C(F)(F)F)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 16, 1, 1, 1, 1, 5, 15, 15, 15, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 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 105 conformations in input total number of sets (complete confs): 105 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 9, 24, 73, 105, 105, 105, 105, 105, 105, 105, 105, 105, 105, 105, 105, 105, 1, 1, 9, 9, 24, 24, 73, 105, 105, 105] 105 rigid atoms, others: [0, 1, 2, 3, 4, 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]) total number of confs: 421 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567786 none O=C1N=C(CCNS(=O)(=O)C2=C(Cl)C=CC=C2C(F)(F)F)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 16, 1, 1, 1, 1, 5, 15, 15, 15, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 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 105 conformations in input total number of sets (complete confs): 105 using faster count positions algorithm for large data unique positions, atoms: [105, 105, 105, 61, 31, 5, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 105, 105, 61, 61, 31, 31, 5, 1, 1, 1] 105 rigid atoms, others: [7, 10, 11, 12, 13, 14, 15, 16, 17, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 354 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567786 /scratch/stefan/7901150/working /scratch/stefan/7901150 mkdir: created directory `1' /scratch/stefan/7901150/working/building/REAL300025567786/1 /scratch/stefan/7901150/working/building/REAL300025567786 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 1 (index: 304) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/304 `/scratch/stefan/7901150/working/3D/304' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CC[N-]S(=O)(=O)C2=C(Cl)C=CC=C2C(F)(F)F)[N-]O1) `REAL300025567786.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025567786.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567786/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567786 none O=C1N=C(CC[N-]S(=O)(=O)C2=C(Cl)C=CC=C2C(F)(F)F)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 16, 1, 1, 1, 1, 5, 15, 15, 15, 8, 12, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [1, 1, 1, 1, 1, 9, 9, 24, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 1, 1, 9, 9, 9, 9, 45, 45, 45] 45 rigid atoms, others: [0, 1, 2, 3, 4, 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]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567786 none O=C1N=C(CC[N-]S(=O)(=O)C2=C(Cl)C=CC=C2C(F)(F)F)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 16, 1, 1, 1, 1, 5, 15, 15, 15, 8, 12, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [45, 45, 45, 21, 19, 5, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 45, 45, 21, 21, 19, 19, 1, 1, 1] 45 rigid atoms, others: [7, 10, 11, 12, 13, 14, 15, 16, 17, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 122 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567786 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567786 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 1: /scratch/stefan/7901150/working/building/REAL300025567786/1.* 0: /scratch/stefan/7901150/working/building/REAL300025567786/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567786 Building REAL300025567787 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567787' /scratch/stefan/7901150/working/building/REAL300025567787 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567787 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567787/0 /scratch/stefan/7901150/working/building/REAL300025567787 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 305) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/305 `/scratch/stefan/7901150/working/3D/305' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=C(F)C=CC=C1S(=O)(=O)NCCC1=NC(=O)O[N-]1) `REAL300025567787.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567787.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567787/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567787 none N#CC1=C(F)C=CC=C1S(=O)(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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: [8, 1, 1, 1, 15, 1, 1, 1, 1, 14, 11, 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, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 5, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 13, 63, 95, 201, 201, 201, 201, 201, 1, 1, 1, 13, 65, 65, 95, 95] 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]) total number of confs: 588 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567787 none N#CC1=C(F)C=CC=C1S(=O)(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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: [8, 1, 1, 1, 15, 1, 1, 1, 1, 14, 11, 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, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 5, 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: [201, 201, 201, 201, 201, 201, 201, 201, 167, 104, 167, 167, 24, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 104, 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]) total number of confs: 697 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567787 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567787 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567787/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567787 Building REAL300025567788 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567788' /scratch/stefan/7901150/working/building/REAL300025567788 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567788 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567788/0 /scratch/stefan/7901150/working/building/REAL300025567788 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 306) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/306 `/scratch/stefan/7901150/working/3D/306' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C1CCOCC1)S(=O)(=O)NCCC1=NC(=O)O[N-]1) `REAL300025567788.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567788.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567788/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567788 none CN(C1CCOCC1)S(=O)(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', '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, 5, 5, 5, 12, 5, 5, 14, 11, 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, 6, 6, 4, 7, 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, 12, 12, 12, 37, 88, 108, 201, 201, 201, 201, 201, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 88, 88, 108, 108] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 32, 34, 35, 36, 33, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22]) total number of confs: 632 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567788 none CN(C1CCOCC1)S(=O)(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', '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, 5, 5, 5, 12, 5, 5, 14, 11, 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, 6, 6, 4, 7, 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: [163, 83, 163, 201, 201, 201, 201, 201, 51, 83, 83, 16, 8, 1, 1, 1, 1, 1, 1, 1, 163, 163, 163, 201, 201, 201, 201, 201, 201, 201, 201, 201, 51, 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: 757 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567788 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567788 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567788/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567788 Building REAL300025567789 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567789' /scratch/stefan/7901150/working/building/REAL300025567789 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567789 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567789/0 /scratch/stefan/7901150/working/building/REAL300025567789 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 307) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/307 `/scratch/stefan/7901150/working/3D/307' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1C=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=N1) `REAL300025567789.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567789.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567789/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567789 none CC(C)N1C=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 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, 6, 6, 4, 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, 1, 11, 1, 1, 1, 1, 2, 2, 2, 9, 41, 71, 177, 177, 177, 177, 177, 1, 1, 11, 11, 11, 11, 11, 11, 11, 1, 9, 41, 41, 71, 71, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 33, 18, 19, 27] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32]) total number of confs: 515 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567789 none CC(C)N1C=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 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, 6, 6, 4, 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, 177, 201, 177, 177, 124, 70, 124, 124, 20, 8, 1, 1, 1, 1, 1, 1, 1, 177, 177, 201, 201, 201, 201, 201, 201, 201, 177, 70, 20, 20, 8, 8, 177] 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: 748 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567789 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567789 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567789/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567789 Building REAL300025567790 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567790' /scratch/stefan/7901150/working/building/REAL300025567790 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567790 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567790/0 /scratch/stefan/7901150/working/building/REAL300025567790 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 308) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/308 `/scratch/stefan/7901150/working/3D/308' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2=CC3=CC=CN=C3C=C2)[N-]O1) `REAL300025567790.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567790.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567790/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567790 none O=C1N=C(CCNS(=O)(=O)C2=CC3=CC=CN=C3C=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 3, 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: [1, 1, 1, 1, 1, 9, 25, 84, 123, 123, 123, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 9, 9, 25, 25, 84, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 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, 32]) total number of confs: 642 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567790 none O=C1N=C(CCNS(=O)(=O)C2=CC3=CC=CN=C3C=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 3, 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: [201, 201, 201, 94, 56, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 94, 94, 56, 56, 9, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 578 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567790 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567790 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567790/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567790 Building REAL300025567791 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567791' /scratch/stefan/7901150/working/building/REAL300025567791 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567791 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567791/0 /scratch/stefan/7901150/working/building/REAL300025567791 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 309) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/309 `/scratch/stefan/7901150/working/3D/309' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CN1C=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=N1) `REAL300025567791.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567791.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567791/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567791 none COC(=O)CN1C=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 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, 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 106 conformations in input total number of sets (complete confs): 106 using faster count positions algorithm for large data unique positions, atoms: [54, 54, 8, 54, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 31, 31, 31, 31, 31, 1, 1, 54, 54, 54, 8, 8, 1, 7, 7, 7, 7, 7, 1] 106 rigid atoms, others: [33, 4, 5, 6, 7, 8, 20, 21, 27] set([0, 1, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567791 none COC(=O)CN1C=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 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, 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 106 conformations in input total number of sets (complete confs): 106 using faster count positions algorithm for large data unique positions, atoms: [106, 106, 57, 106, 31, 31, 31, 25, 15, 25, 25, 15, 7, 1, 1, 1, 1, 1, 1, 1, 31, 31, 106, 106, 106, 57, 57, 31, 15, 15, 15, 7, 7, 31] 106 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: 452 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567791 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567791 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567791/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567791 Building REAL300025567792 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567792' /scratch/stefan/7901150/working/building/REAL300025567792 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567792 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567792/0 /scratch/stefan/7901150/working/building/REAL300025567792 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 310) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/310 `/scratch/stefan/7901150/working/3D/310' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C1=NC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=CN1) `REAL300025567792.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567792.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567792/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567792 none CC(C)C1=NC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=CN1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 1, 14, 11, 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, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 1, 1, 1, 1, 6, 6, 6, 19, 61, 69, 171, 171, 171, 171, 171, 1, 1, 13, 13, 13, 13, 13, 13, 13, 19, 61, 61, 69, 69, 1, 1] 201 rigid atoms, others: [32, 1, 3, 4, 5, 6, 33, 18, 19] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 480 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567792 none CC(C)C1=NC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=CN1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 1, 14, 11, 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, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need 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, 110, 78, 110, 110, 20, 8, 1, 1, 1, 1, 1, 1, 1, 171, 171, 201, 201, 201, 201, 201, 201, 201, 78, 20, 20, 8, 8, 171, 171] 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: 702 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567792 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567792 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567792/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567792 Building REAL300025567793 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567793' /scratch/stefan/7901150/working/building/REAL300025567793 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567793 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567793/0 /scratch/stefan/7901150/working/building/REAL300025567793 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 311) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/311 `/scratch/stefan/7901150/working/3D/311' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)CC2=CC=C(Br)C=C2)[N-]O1) `REAL300025567793.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567793.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567793/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567793 none O=C1N=C(CCNS(=O)(=O)CC2=CC=C(Br)C=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', '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', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 5, 1, 1, 1, 1, 17, 1, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 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: [1, 1, 1, 1, 1, 9, 25, 95, 131, 131, 131, 201, 201, 201, 201, 201, 201, 201, 1, 1, 9, 9, 25, 25, 95, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 18, 19] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 809 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567793 none O=C1N=C(CCNS(=O)(=O)CC2=CC=C(Br)C=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', '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', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 5, 1, 1, 1, 1, 17, 1, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 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: [201, 201, 201, 123, 98, 36, 13, 3, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 123, 123, 98, 98, 36, 3, 3, 1, 1, 1, 1] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 657 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567793 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567793 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567793/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567793 Building REAL300025567794 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567794' /scratch/stefan/7901150/working/building/REAL300025567794 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567794 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567794/0 /scratch/stefan/7901150/working/building/REAL300025567794 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 312) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/312 `/scratch/stefan/7901150/working/3D/312' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2=CC3=CC=C(Cl)N=C3C=C2F)[N-]O1) `REAL300025567794.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567794.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567794/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567794 none O=C1N=C(CCNS(=O)(=O)C2=CC3=CC=C(Cl)N=C3C=C2F)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 16, 8, 1, 1, 1, 15, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 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: [1, 1, 1, 1, 1, 9, 23, 78, 134, 134, 134, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 9, 9, 23, 23, 78, 201, 201, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 22, 23] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 633 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567794 none O=C1N=C(CCNS(=O)(=O)C2=CC3=CC=C(Cl)N=C3C=C2F)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 16, 8, 1, 1, 1, 15, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 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: [201, 201, 201, 107, 77, 25, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 107, 107, 77, 77, 25, 1, 1, 1, 1] 201 rigid atoms, others: [32, 7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 633 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567794 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567794 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567794/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567794 Building REAL300025567795 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567795' /scratch/stefan/7901150/working/building/REAL300025567795 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567795 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567795/0 /scratch/stefan/7901150/working/building/REAL300025567795 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 313) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/313 `/scratch/stefan/7901150/working/3D/313' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=NN1C1=CC=CC=N1) `REAL300025567795.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567795/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567795 none CC1=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=NN1C1=CC=CC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 8, 1, 1, 1, 1, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 5, 5, 5, 15, 54, 91, 201, 201, 201, 201, 201, 1, 1, 1, 1, 4, 4, 4, 4, 4, 2, 2, 2, 15, 56, 56, 91, 91, 1, 4, 4, 4, 4] 201 rigid atoms, others: [0, 1, 2, 3, 32, 15, 16, 17, 18] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567795 none CC1=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=NN1C1=CC=CC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 8, 1, 1, 1, 1, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 163, 92, 163, 163, 24, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 92, 25, 25, 8, 8, 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]) 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567795 none CC1=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=NN1C1=CC=CC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 8, 1, 1, 1, 1, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 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] 0 hydrogens 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, 9, 9, 9, 21, 68, 107, 201, 201, 201, 201, 201, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 21, 70, 70, 107, 107, 4, 1, 1, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 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]) total number of confs: 631 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567795 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567795 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567795/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567795 Building REAL300025567796 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567796' /scratch/stefan/7901150/working/building/REAL300025567796 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567796 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567796/0 /scratch/stefan/7901150/working/building/REAL300025567796 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 314) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/314 `/scratch/stefan/7901150/working/3D/314' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(OC2=CC=C(S(=O)(=O)NCCC3=NC(=O)O[N-]3)C=C2)C=C1) `REAL300025567796.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567796/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567796 none COC1=CC=C(OC2=CC=C(S(=O)(=O)NCCC3=NC(=O)O[N-]3)C=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', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 12, 1, 1, 1, 1, 12, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 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, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 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, 8, 11, 11, 9, 10, 15, 15, 15, 30, 73, 98, 201, 201, 201, 201, 201, 11, 11, 1, 1, 2, 2, 2, 1, 1, 11, 11, 30, 73, 73, 98, 98, 11, 11, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 41, 42, 25, 26, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 631 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567796 none COC1=CC=C(OC2=CC=C(S(=O)(=O)NCCC3=NC(=O)O[N-]3)C=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', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 12, 1, 1, 1, 1, 12, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 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, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 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, 5, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 25, 42, 115, 115, 115, 115, 115, 1, 1, 11, 11, 11, 11, 11, 11, 11, 1, 1, 9, 25, 25, 42, 42, 1, 1, 11, 11] 201 rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 40, 23, 24, 39] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 41, 42]) total number of confs: 318 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567796 none COC1=CC=C(OC2=CC=C(S(=O)(=O)NCCC3=NC(=O)O[N-]3)C=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', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 12, 1, 1, 1, 1, 12, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 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, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 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, 200, 115, 86, 115, 115, 67, 53, 67, 67, 18, 8, 1, 1, 1, 1, 1, 1, 1, 115, 115, 201, 201, 201, 201, 201, 201, 201, 115, 115, 53, 19, 19, 8, 8, 115, 115, 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]) total number of confs: 649 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567796 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567796 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567796/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567796 Building REAL300025567797 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567797' /scratch/stefan/7901150/working/building/REAL300025567797 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567797 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567797/0 /scratch/stefan/7901150/working/building/REAL300025567797 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 315) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/315 `/scratch/stefan/7901150/working/3D/315' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC(C(F)(F)F)=CC=C1S(=O)(=O)NCCC1=NC(=O)O[N-]1) `REAL300025567797.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567797.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567797/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567797 none N#CC1=CC(C(F)(F)F)=CC=C1S(=O)(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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: [8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 14, 11, 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, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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, 1, 2, 2, 2, 1, 1, 1, 1, 4, 4, 4, 13, 59, 91, 193, 193, 193, 193, 193, 1, 1, 1, 13, 61, 61, 91, 91] 193 rigid atoms, others: [0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 24, 25, 26] set([6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31]) total number of confs: 575 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567797 none N#CC1=CC(C(F)(F)F)=CC=C1S(=O)(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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: [8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 14, 11, 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, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 193 conformations in input total number of sets (complete confs): 193 using faster count positions algorithm for large data unique positions, atoms: [193, 193, 193, 193, 193, 193, 193, 193, 193, 193, 193, 173, 109, 173, 173, 24, 8, 1, 1, 1, 1, 1, 1, 1, 193, 193, 193, 109, 24, 24, 8, 8] 193 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]) total number of confs: 685 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567797 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567797 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567797/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567797 Building REAL300025567798 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567798' /scratch/stefan/7901150/working/building/REAL300025567798 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567798 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567798/0 /scratch/stefan/7901150/working/building/REAL300025567798 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 316) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/316 `/scratch/stefan/7901150/working/3D/316' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC=CC(CC)=C1S(=O)(=O)NCCC1=NC(=O)O[N-]1) `REAL300025567798.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567798.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567798/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567798 none CCC1=CC=CC(CC)=C1S(=O)(=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', 'C.3', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', '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, 1, 1, 1, 1, 1, 5, 5, 1, 14, 11, 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, 6, 6, 4, 7, 7, 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, 6, 1, 1, 8, 8, 8, 13, 47, 75, 188, 188, 188, 188, 188, 5, 5, 5, 5, 5, 1, 1, 1, 6, 6, 6, 6, 6, 13, 47, 47, 75, 75] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 9, 10, 27, 28, 29] set([0, 8, 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: 542 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567798 none CCC1=CC=CC(CC)=C1S(=O)(=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', 'C.3', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', '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, 1, 1, 1, 1, 1, 5, 5, 1, 14, 11, 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, 6, 6, 4, 7, 7, 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: [190, 188, 188, 188, 183, 188, 188, 188, 201, 162, 94, 162, 162, 24, 8, 1, 1, 1, 1, 1, 1, 1, 190, 190, 190, 190, 190, 188, 183, 188, 201, 201, 201, 201, 201, 94, 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, 34, 35, 36, 37, 38, 39]) total number of confs: 796 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567798 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567798 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567798/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567798 Building REAL300025567799 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567799' /scratch/stefan/7901150/working/building/REAL300025567799 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567799 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567799/0 /scratch/stefan/7901150/working/building/REAL300025567799 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 317) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/317 `/scratch/stefan/7901150/working/3D/317' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2=CC(F)=C(F)C(F)=C2)[N-]O1) `REAL300025567799.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567799/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567799 none O=C1N=C(CCNS(=O)(=O)C2=CC(F)=C(F)C(F)=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 15, 1, 15, 1, 15, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 9, 25, 92, 136, 136, 136, 136, 136, 136, 136, 136, 136, 136, 136, 1, 1, 9, 9, 25, 25, 92, 136, 136] 136 rigid atoms, others: [0, 1, 2, 3, 4, 19, 20] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 534 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567799 none O=C1N=C(CCNS(=O)(=O)C2=CC(F)=C(F)C(F)=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 15, 1, 15, 1, 15, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 55, 29, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 136, 136, 55, 55, 29, 29, 5, 1, 1] 136 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27] set([0, 1, 2, 3, 4, 5, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 350 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567799 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567799 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567799/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567799 Building REAL300025567800 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567800' /scratch/stefan/7901150/working/building/REAL300025567800 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567800 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567800/0 /scratch/stefan/7901150/working/building/REAL300025567800 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 318) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/318 `/scratch/stefan/7901150/working/3D/318' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=CC=C1CS(=O)(=O)NCCC1=NC(=O)O[N-]1) `REAL300025567800.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567800.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567800/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567800 none COC(=O)C1=CC=CC=C1CS(=O)(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', '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, 11, 1, 1, 1, 1, 1, 1, 5, 14, 11, 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, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 1, 9, 1, 1, 1, 1, 1, 1, 1, 5, 14, 14, 14, 33, 74, 74, 175, 175, 175, 175, 175, 9, 9, 9, 1, 1, 1, 1, 5, 5, 33, 74, 74, 74, 74] 201 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 26, 27, 28, 29] set([0, 1, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 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 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567800 none COC(=O)C1=CC=CC=C1CS(=O)(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', '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, 11, 1, 1, 1, 1, 1, 1, 5, 14, 11, 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, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 175, 201, 175, 175, 175, 175, 175, 116, 64, 37, 64, 64, 8, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 175, 175, 175, 175, 116, 116, 37, 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]) total number of confs: 693 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567800 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567800 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567800/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567800 Building REAL300025567801 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567801' /scratch/stefan/7901150/working/building/REAL300025567801 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567801 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567801/0 /scratch/stefan/7901150/working/building/REAL300025567801 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 319) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/319 `/scratch/stefan/7901150/working/3D/319' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)C1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1) `REAL300025567801.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567801.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567801/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567801 none CC(C)C(=O)C1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.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, 11, 1, 1, 1, 1, 14, 11, 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, 7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 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, 6, 10, 1, 6, 1, 1, 1, 1, 1, 2, 2, 2, 9, 29, 41, 126, 126, 126, 126, 126, 1, 1, 11, 11, 11, 11, 10, 10, 10, 1, 1, 9, 29, 29, 41, 41, 1, 1] 201 rigid atoms, others: [3, 5, 6, 7, 8, 9, 21, 22, 38, 37, 30, 31] set([0, 1, 2, 4, 10, 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: 342 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567801 none CC(C)C(=O)C1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.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, 11, 1, 1, 1, 1, 14, 11, 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, 7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 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, 125, 201, 126, 126, 126, 89, 67, 89, 89, 18, 8, 1, 1, 1, 1, 1, 1, 1, 126, 126, 201, 201, 201, 201, 201, 201, 201, 126, 126, 67, 19, 19, 8, 8, 126, 126] 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: 704 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567801 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567801 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567801/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567801 Building REAL300025567802 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567802' /scratch/stefan/7901150/working/building/REAL300025567802 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567802 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567802/0 /scratch/stefan/7901150/working/building/REAL300025567802 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 320) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/320 `/scratch/stefan/7901150/working/3D/320' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=CN1C) `REAL300025567802.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567802.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567802/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567802 none COC(=O)C1=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=CN1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 5, 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, 6, 4, 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, 1, 4, 1, 1, 1, 1, 2, 2, 2, 9, 45, 73, 151, 151, 151, 151, 151, 1, 1, 1, 4, 4, 4, 1, 9, 45, 45, 73, 73, 1, 2, 2, 2] 201 rigid atoms, others: [2, 4, 5, 6, 7, 19, 20, 21, 25, 31] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 26, 27, 28, 29, 30, 32, 33, 34]) total number of confs: 471 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567802 none COC(=O)C1=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=CN1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 5, 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, 6, 4, 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, 151, 201, 151, 151, 89, 62, 89, 89, 22, 8, 1, 1, 1, 1, 1, 1, 1, 151, 151, 151, 201, 201, 201, 151, 62, 22, 22, 8, 8, 151, 151, 151, 151] 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]) total number of confs: 680 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567802 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567802 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567802/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567802 Building REAL300025567803 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567803' /scratch/stefan/7901150/working/building/REAL300025567803 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567803 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567803/0 /scratch/stefan/7901150/working/building/REAL300025567803 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 321) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/321 `/scratch/stefan/7901150/working/3D/321' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)C1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1) `REAL300025567803.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567803.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567803/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567803 none CCC(C)(C)C1=CC=C(S(=O)(=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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 1, 1, 1, 1, 14, 11, 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, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 2, 2, 9, 25, 45, 100, 100, 100, 100, 100, 1, 1, 6, 6, 6, 6, 6, 4, 4, 4, 4, 4, 4, 1, 1, 9, 25, 25, 45, 45, 1, 1] 201 rigid atoms, others: [34, 35, 5, 6, 7, 8, 9, 42, 2, 21, 22, 41] set([0, 1, 3, 4, 10, 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: 316 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567803 none CCC(C)(C)C1=CC=C(S(=O)(=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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 1, 1, 1, 1, 14, 11, 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, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 197, 51, 197, 197, 51, 100, 100, 51, 39, 51, 51, 14, 8, 1, 1, 1, 1, 1, 1, 1, 100, 100, 201, 201, 201, 201, 201, 197, 197, 197, 197, 197, 197, 100, 100, 39, 14, 15, 8, 8, 100, 100] 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: 1650 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567803 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567803 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567803/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567803 Building REAL300025567804 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567804' /scratch/stefan/7901150/working/building/REAL300025567804 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567804 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567804/0 /scratch/stefan/7901150/working/building/REAL300025567804 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 322) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/322 `/scratch/stefan/7901150/working/3D/322' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=NN=C1C1=CC=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=C1) `REAL300025567804.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567804.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567804/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567804 none CN1N=NN=C1C1=CC=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [5, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 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, 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, 7, 7, 1, 7, 7, 9, 9, 9, 29, 77, 99, 201, 201, 201, 201, 201, 7, 2, 2, 2, 7, 7, 1, 29, 77, 77, 99, 99, 7] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 609 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567804 none CN1N=NN=C1C1=CC=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [5, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 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, 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, 7, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 39, 61, 160, 160, 160, 160, 160, 1, 7, 7, 7, 1, 1, 1, 9, 39, 39, 61, 61, 1] 201 rigid atoms, others: [35, 5, 6, 7, 8, 9, 10, 11, 23, 27, 28, 29] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567804 none CN1N=NN=C1C1=CC=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [5, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 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, 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, 160, 160, 160, 160, 160, 130, 93, 130, 130, 24, 8, 1, 1, 1, 1, 1, 1, 1, 160, 201, 201, 201, 160, 160, 160, 93, 25, 25, 8, 8, 160] 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: 630 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567804 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567804 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567804/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567804 Building REAL300025567805 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567805' /scratch/stefan/7901150/working/building/REAL300025567805 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567805 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567805/0 /scratch/stefan/7901150/working/building/REAL300025567805 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 323) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/323 `/scratch/stefan/7901150/working/3D/323' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2=CN(C3=CC=CC=C3F)N=C2)[N-]O1) `REAL300025567805.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567805.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567805/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567805 none O=C1N=C(CCNS(=O)(=O)C2=CN(C3=CC=CC=C3F)N=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.2', 'C.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 15, 8, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 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: [1, 1, 1, 1, 1, 9, 18, 50, 88, 88, 88, 156, 156, 156, 201, 201, 193, 201, 201, 201, 156, 156, 1, 1, 9, 9, 18, 18, 50, 156, 201, 201, 201, 201, 156] 201 rigid atoms, others: [0, 1, 2, 3, 4, 22, 23] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 610 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567805 none O=C1N=C(CCNS(=O)(=O)C2=CN(C3=CC=CC=C3F)N=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.2', 'C.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 15, 8, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 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: [156, 156, 156, 75, 41, 9, 3, 1, 3, 3, 1, 1, 1, 1, 6, 6, 2, 6, 6, 6, 1, 1, 156, 156, 75, 75, 41, 41, 9, 1, 6, 6, 6, 6, 1] 201 rigid atoms, others: [34, 7, 10, 11, 12, 13, 20, 21, 29] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33]) 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567805 none O=C1N=C(CCNS(=O)(=O)C2=CN(C3=CC=CC=C3F)N=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.2', 'C.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 15, 8, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 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: [201, 201, 201, 120, 87, 33, 11, 6, 11, 11, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 201, 201, 120, 120, 87, 87, 33, 6, 1, 1, 1, 1, 6] 201 rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34]) total number of confs: 648 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567805 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567805 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567805/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567805 Building REAL300025567806 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567806' /scratch/stefan/7901150/working/building/REAL300025567806 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567806 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567806/0 /scratch/stefan/7901150/working/building/REAL300025567806 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 324) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/324 `/scratch/stefan/7901150/working/3D/324' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=NN1C1=CC=C(Cl)C=C1) `REAL300025567806.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567806.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567806/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567806 none CC1=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=NN1C1=CC=C(Cl)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations 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, 13, 38, 63, 199, 199, 197, 199, 199, 1, 1, 1, 1, 5, 5, 1, 1, 5, 5, 2, 2, 2, 13, 40, 40, 63, 63, 1, 5, 5, 5, 5] 201 rigid atoms, others: [0, 1, 2, 3, 33, 15, 16, 17, 18] set([4, 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]) total number of confs: 482 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567806 none CC1=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=NN1C1=CC=C(Cl)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [199, 199, 183, 98, 183, 183, 24, 8, 1, 1, 1, 1, 1, 1, 1, 199, 199, 199, 199, 201, 201, 199, 199, 201, 201, 199, 199, 199, 98, 24, 25, 8, 8, 199, 201, 201, 199, 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]) total number of confs: 751 number of broken/clashed sets: 12 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567806 none CC1=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=NN1C1=CC=C(Cl)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 13, 13, 13, 24, 71, 107, 201, 201, 199, 201, 201, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 24, 73, 73, 107, 107, 5, 1, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 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]) total number of confs: 628 number of broken/clashed sets: 12 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567806 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567806 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567806/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567806 Building REAL300025567807 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567807' /scratch/stefan/7901150/working/building/REAL300025567807 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567807 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567807/0 /scratch/stefan/7901150/working/building/REAL300025567807 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 325) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/325 `/scratch/stefan/7901150/working/3D/325' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(Br)=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)S1) `REAL300025567807.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567807.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567807/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567807 none CC1=CC(Br)=C(S(=O)(=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', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 14, 11, 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, 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, 8, 8, 8, 17, 65, 104, 201, 201, 201, 201, 201, 1, 2, 2, 2, 1, 17, 65, 65, 104, 104] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 18, 22] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 23, 24, 25, 26, 27]) total number of confs: 634 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567807 none CC1=CC(Br)=C(S(=O)(=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', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 14, 11, 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, 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, 168, 91, 168, 168, 23, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 91, 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]) total number of confs: 696 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567807 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567807 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567807/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567807 Building REAL300025567808 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567808' /scratch/stefan/7901150/working/building/REAL300025567808 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567808 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567808/0 /scratch/stefan/7901150/working/building/REAL300025567808 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 326) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/326 `/scratch/stefan/7901150/working/3D/326' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2=CC=C(Br)C(F)=C2)[N-]O1) `REAL300025567808.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567808.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567808/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567808 none O=C1N=C(CCNS(=O)(=O)C2=CC=C(Br)C(F)=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 17, 1, 15, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 9, 25, 82, 118, 118, 118, 201, 201, 201, 201, 201, 201, 201, 1, 1, 9, 9, 25, 25, 82, 201, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 18, 19] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 638 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567808 none O=C1N=C(CCNS(=O)(=O)C2=CC=C(Br)C(F)=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 17, 1, 15, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 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: [201, 201, 201, 91, 51, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 91, 91, 51, 51, 9, 1, 1, 1] 201 rigid atoms, others: [7, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 566 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567808 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567808 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567808/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567808 Building REAL300025567809 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567809' /scratch/stefan/7901150/working/building/REAL300025567809 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567809 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567809/0 /scratch/stefan/7901150/working/building/REAL300025567809 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 327) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/327 `/scratch/stefan/7901150/working/3D/327' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N(C)C1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1) `REAL300025567809.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567809/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567809 none CC(=O)N(C)C1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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: [5, 1, 11, 8, 5, 1, 1, 1, 1, 14, 11, 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, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 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 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [12, 6, 12, 1, 6, 1, 1, 1, 1, 1, 2, 2, 2, 9, 21, 21, 49, 49, 49, 49, 49, 1, 1, 12, 12, 12, 6, 6, 6, 1, 1, 9, 21, 21, 21, 21, 1, 1] 100 rigid atoms, others: [3, 36, 5, 6, 7, 8, 9, 21, 22, 29, 30, 37] set([0, 1, 2, 4, 10, 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: 165 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567809 none CC(=O)N(C)C1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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: [5, 1, 11, 8, 5, 1, 1, 1, 1, 14, 11, 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, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 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 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [100, 90, 100, 49, 90, 49, 49, 49, 33, 25, 33, 33, 11, 5, 1, 1, 1, 1, 1, 1, 1, 49, 49, 100, 100, 100, 90, 90, 90, 49, 49, 25, 12, 11, 5, 5, 49, 49] 100 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: 340 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567809 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567809 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567809/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567809 Building REAL300025567810 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567810' /scratch/stefan/7901150/working/building/REAL300025567810 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567810 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567810/0 /scratch/stefan/7901150/working/building/REAL300025567810 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 328) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/328 `/scratch/stefan/7901150/working/3D/328' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=CC(C)=C1F) `REAL300025567810.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567810.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567810/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567810 none CC1=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=CC(C)=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 5, 1, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 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 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, 2, 2, 2, 6, 30, 58, 142, 142, 142, 142, 142, 1, 1, 1, 1, 1, 2, 2, 2, 1, 6, 30, 30, 58, 58, 1, 2, 2, 2] 142 rigid atoms, others: [0, 1, 2, 3, 4, 16, 17, 18, 19, 20, 24, 30] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 25, 26, 27, 28, 29, 31, 32, 33]) total number of confs: 381 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567810 none CC1=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=CC(C)=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 5, 1, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 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 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, 94, 142, 142, 22, 8, 1, 1, 1, 1, 1, 1, 1, 142, 142, 142, 142, 142, 142, 142, 142, 142, 94, 22, 22, 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]) total number of confs: 549 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567810 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567810 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567810/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567810 Building REAL300025567811 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567811' /scratch/stefan/7901150/working/building/REAL300025567811 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567811 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567811/0 /scratch/stefan/7901150/working/building/REAL300025567811 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 329) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/329 `/scratch/stefan/7901150/working/3D/329' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2=CC=C(F)C(Br)=C2)[N-]O1) `REAL300025567811.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567811.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567811/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567811 none O=C1N=C(CCNS(=O)(=O)C2=CC=C(F)C(Br)=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Br', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 15, 1, 17, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 9, 25, 79, 117, 117, 117, 201, 201, 201, 201, 201, 201, 201, 1, 1, 9, 9, 25, 25, 79, 201, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 18, 19] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 644 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567811 none O=C1N=C(CCNS(=O)(=O)C2=CC=C(F)C(Br)=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Br', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 15, 1, 17, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 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: [201, 201, 201, 88, 51, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 88, 88, 51, 51, 9, 1, 1, 1] 201 rigid atoms, others: [7, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 555 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567811 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567811 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567811/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567811 Building REAL300025567812 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567812' /scratch/stefan/7901150/working/building/REAL300025567812 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567812 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567812/0 /scratch/stefan/7901150/working/building/REAL300025567812 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 330) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/330 `/scratch/stefan/7901150/working/3D/330' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C(Cl)=C1Cl) `REAL300025567812.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567812.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567812/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567812 none COC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C(Cl)=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 12, 1, 1, 1, 1, 14, 11, 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, 3, 7, 7, 7, 7, 7, 6, 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, 5, 5, 5, 9, 35, 58, 185, 185, 185, 185, 185, 1, 1, 1, 1, 4, 4, 4, 1, 1, 9, 35, 35, 58, 58] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 18, 19, 20, 21, 25, 26] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 27, 28, 29, 30, 31]) total number of confs: 435 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567812 none COC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C(Cl)=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 12, 1, 1, 1, 1, 14, 11, 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, 3, 7, 7, 7, 7, 7, 6, 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, 185, 185, 185, 185, 182, 102, 182, 182, 24, 8, 1, 1, 1, 1, 1, 1, 1, 185, 185, 185, 185, 201, 201, 201, 185, 185, 102, 25, 25, 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]) total number of confs: 743 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567812 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567812 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567812/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567812 Building REAL300025567813 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567813' /scratch/stefan/7901150/working/building/REAL300025567813 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567813 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567813/0 /scratch/stefan/7901150/working/building/REAL300025567813 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 331) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/331 `/scratch/stefan/7901150/working/3D/331' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C1=NC2=CC=C(S(=O)(=O)NCCC3=NC(=O)O[N-]3)C=C2S1) `REAL300025567813.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567813/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567813 none CC(C)(C)C1=NC2=CC=C(S(=O)(=O)NCCC3=NC(=O)O[N-]3)C=C2S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 14, 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, 6, 6, 4, 7, 7, 7, 7, 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, 1, 4, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 41, 74, 201, 201, 201, 201, 201, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 9, 41, 41, 74, 74, 1] 201 rigid atoms, others: [1, 34, 35, 4, 5, 6, 7, 8, 9, 10, 41, 22, 23, 24] set([0, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40]) total number of confs: 527 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567813 none CC(C)(C)C1=NC2=CC=C(S(=O)(=O)NCCC3=NC(=O)O[N-]3)C=C2S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 14, 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, 6, 6, 4, 7, 7, 7, 7, 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, 109, 70, 109, 109, 21, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 70, 21, 21, 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, 40, 41]) total number of confs: 627 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567813 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567813 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567813/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567813 Building REAL300025567814 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567814' /scratch/stefan/7901150/working/building/REAL300025567814 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567814 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567814/0 /scratch/stefan/7901150/working/building/REAL300025567814 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 332) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/332 `/scratch/stefan/7901150/working/3D/332' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC=C1N1C=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=N1) `REAL300025567814.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567814.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567814/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567814 none COC1=CC=CC=C1N1C=C(S(=O)(=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.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 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, 6, 6, 4, 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, 1, 6, 6, 6, 11, 11, 11, 31, 76, 104, 201, 201, 201, 201, 201, 6, 6, 4, 4, 4, 1, 1, 1, 1, 6, 31, 76, 76, 104, 104, 6] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 28, 29, 30, 31] set([0, 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]) total number of confs: 621 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567814 none COC1=CC=CC=C1N1C=C(S(=O)(=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.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 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, 6, 6, 4, 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, 6, 6, 6, 5, 6, 6, 1, 1, 1, 1, 1, 2, 2, 2, 9, 40, 63, 133, 133, 133, 133, 133, 1, 1, 9, 9, 9, 6, 5, 6, 6, 1, 9, 40, 40, 63, 63, 1] 201 rigid atoms, others: [32, 38, 7, 8, 9, 10, 11, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567814 none COC1=CC=CC=C1N1C=C(S(=O)(=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.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 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, 6, 6, 4, 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, 133, 133, 133, 95, 62, 95, 95, 22, 8, 1, 1, 1, 1, 1, 1, 1, 133, 133, 201, 201, 201, 201, 201, 201, 201, 133, 62, 22, 22, 8, 8, 133] 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: 562 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567814 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567814 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567814/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567814 Building REAL300025567815 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567815' /scratch/stefan/7901150/working/building/REAL300025567815 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567815 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567815/0 /scratch/stefan/7901150/working/building/REAL300025567815 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 333) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/333 `/scratch/stefan/7901150/working/3D/333' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC(Cl)=CC=C1S(=O)(=O)NCCC1=NC(=O)O[N-]1) `REAL300025567815.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567815/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567815 none N#CC1=CC(Cl)=CC=C1S(=O)(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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: [8, 1, 1, 1, 1, 16, 1, 1, 1, 14, 11, 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, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 5, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 13, 64, 100, 201, 201, 201, 201, 201, 1, 1, 1, 13, 66, 66, 100, 100] 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]) total number of confs: 600 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567815 none N#CC1=CC(Cl)=CC=C1S(=O)(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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: [8, 1, 1, 1, 1, 16, 1, 1, 1, 14, 11, 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, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 5, 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: [199, 201, 201, 201, 201, 201, 201, 201, 171, 109, 171, 171, 24, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 109, 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]) total number of confs: 689 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567815 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567815 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567815/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567815 Building REAL300025567816 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567816' /scratch/stefan/7901150/working/building/REAL300025567816 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025567816 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567816/0 /scratch/stefan/7901150/working/building/REAL300025567816 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 334) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/334 `/scratch/stefan/7901150/working/3D/334' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CC[N-]S(=O)(=O)C2=C(Cl)C=C(Cl)C=C2[N+](=O)[O-])[N-]O1) `REAL300025567816.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567816.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567816/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567816 none O=C1N=C(CC[N-]S(=O)(=O)C2=C(Cl)C=C(Cl)C=C2[N+](=O)[O-])[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 16, 1, 1, 16, 1, 1, 8, 11, 11, 8, 12, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 3, 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: [1, 1, 1, 1, 1, 9, 15, 33, 51, 51, 51, 51, 51, 51, 51, 51, 51, 51, 51, 51, 51, 1, 1, 9, 9, 15, 15, 51, 51] 51 rigid atoms, others: [0, 1, 2, 3, 4, 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]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567816 none O=C1N=C(CC[N-]S(=O)(=O)C2=C(Cl)C=C(Cl)C=C2[N+](=O)[O-])[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 16, 1, 1, 16, 1, 1, 8, 11, 11, 8, 12, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 3, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [51, 51, 51, 23, 19, 5, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 51, 51, 23, 23, 19, 19, 1, 1] 51 rigid atoms, others: [7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 140 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567816 /scratch/stefan/7901150/working /scratch/stefan/7901150 mkdir: created directory `1' /scratch/stefan/7901150/working/building/REAL300025567816/1 /scratch/stefan/7901150/working/building/REAL300025567816 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 1 (index: 335) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/335 `/scratch/stefan/7901150/working/3D/335' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2=C(Cl)C=C(Cl)C=C2[N+](=O)[O-])[N-]O1) `REAL300025567816.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025567816.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567816/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567816 none O=C1N=C(CCNS(=O)(=O)C2=C(Cl)C=C(Cl)C=C2[N+](=O)[O-])[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 16, 1, 1, 16, 1, 1, 8, 11, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 9, 22, 48, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 1, 1, 9, 9, 22, 22, 48, 55, 55] 55 rigid atoms, others: [0, 1, 2, 3, 4, 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]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567816 none O=C1N=C(CCNS(=O)(=O)C2=C(Cl)C=C(Cl)C=C2[N+](=O)[O-])[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 16, 1, 1, 16, 1, 1, 8, 11, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [55, 55, 55, 27, 23, 5, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 55, 55, 27, 27, 23, 23, 5, 1, 1] 55 rigid atoms, others: [7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 158 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567816 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567816 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 1: /scratch/stefan/7901150/working/building/REAL300025567816/1.* 0: /scratch/stefan/7901150/working/building/REAL300025567816/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567816 Building REAL300025567817 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567817' /scratch/stefan/7901150/working/building/REAL300025567817 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567817 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567817/0 /scratch/stefan/7901150/working/building/REAL300025567817 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 336) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/336 `/scratch/stefan/7901150/working/3D/336' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=CN1) `REAL300025567817.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567817.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567817/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567817 none COC(=O)C1=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=CN1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 1, 2, 1, 1, 1, 1, 2, 2, 2, 9, 44, 72, 143, 143, 143, 143, 143, 1, 1, 2, 2, 2, 1, 9, 44, 44, 72, 72, 1, 1] 201 rigid atoms, others: [2, 4, 5, 6, 7, 19, 20, 24, 30, 31] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 25, 26, 27, 28, 29]) total number of confs: 448 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567817 none COC(=O)C1=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=CN1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 143, 201, 143, 143, 81, 58, 81, 81, 21, 8, 1, 1, 1, 1, 1, 1, 1, 143, 143, 201, 201, 201, 143, 58, 21, 21, 8, 8, 143, 143] 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: 685 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567817 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567817 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567817/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567817 Building REAL300025567818 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567818' /scratch/stefan/7901150/working/building/REAL300025567818 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567818 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567818/0 /scratch/stefan/7901150/working/building/REAL300025567818 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 337) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/337 `/scratch/stefan/7901150/working/3D/337' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(F)C=CC=C1S(=O)(=O)NCCC1=NC(=O)O[N-]1) `REAL300025567818.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567818.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567818/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567818 none CC1=C(F)C=CC=C1S(=O)(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.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, 15, 1, 1, 1, 1, 14, 11, 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, 6, 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 195 conformations in input total number of sets (complete confs): 195 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 13, 59, 85, 195, 195, 195, 195, 195, 2, 2, 2, 1, 1, 1, 13, 61, 61, 85, 85] 195 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 23, 24, 25] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30]) total number of confs: 512 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567818 none CC1=C(F)C=CC=C1S(=O)(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.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, 15, 1, 1, 1, 1, 14, 11, 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, 6, 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 195 conformations in input total number of sets (complete confs): 195 using faster count positions algorithm for large data unique positions, atoms: [195, 195, 195, 195, 195, 195, 195, 187, 101, 187, 187, 24, 8, 1, 1, 1, 1, 1, 1, 1, 195, 195, 195, 195, 195, 195, 101, 24, 24, 8, 8] 195 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: 741 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567818 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567818 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567818/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567818 Building REAL300025567819 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567819' /scratch/stefan/7901150/working/building/REAL300025567819 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567819 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567819/0 /scratch/stefan/7901150/working/building/REAL300025567819 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 338) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/338 `/scratch/stefan/7901150/working/3D/338' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=CC=C1C) `REAL300025567819.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567819.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567819/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567819 none COC(=O)C1=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 6, 6, 4, 7, 7, 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: [9, 9, 1, 9, 1, 1, 1, 1, 3, 3, 3, 9, 27, 41, 100, 100, 100, 100, 100, 1, 1, 1, 1, 9, 9, 9, 1, 9, 27, 27, 41, 41, 1, 1, 2, 2, 2] 201 rigid atoms, others: [32, 33, 2, 4, 5, 6, 7, 19, 20, 21, 22, 26] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 27, 28, 29, 30, 31, 34, 35, 36]) total number of confs: 302 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567819 none COC(=O)C1=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 6, 6, 4, 7, 7, 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, 100, 201, 100, 100, 62, 44, 62, 62, 14, 8, 1, 1, 1, 1, 1, 1, 1, 100, 100, 100, 100, 201, 201, 201, 100, 44, 14, 14, 8, 8, 100, 100, 100, 100, 100] 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: 655 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567819 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567819 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567819/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567819 Building REAL300025567820 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567820' /scratch/stefan/7901150/working/building/REAL300025567820 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567820 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567820/0 /scratch/stefan/7901150/working/building/REAL300025567820 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 339) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/339 `/scratch/stefan/7901150/working/3D/339' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1Br) `REAL300025567820.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567820.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567820/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567820 none CC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1Br 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.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'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 17, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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, 2, 2, 2, 9, 51, 91, 201, 201, 201, 201, 201, 1, 1, 1, 2, 2, 2, 1, 1, 9, 51, 51, 91, 91, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 17, 18, 19, 23, 24, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 25, 26, 27, 28, 29]) total number of confs: 571 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567820 none CC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1Br 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.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'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 17, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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, 121, 83, 121, 121, 24, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 83, 24, 24, 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]) total number of confs: 641 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567820 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567820 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567820/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567820 Building REAL300025567821 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567821' /scratch/stefan/7901150/working/building/REAL300025567821 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567821 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567821/0 /scratch/stefan/7901150/working/building/REAL300025567821 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 340) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/340 `/scratch/stefan/7901150/working/3D/340' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=CS1) `REAL300025567821.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567821.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567821/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567821 none COC(=O)C1=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=CS1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 14, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 6, 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, 2, 1, 1, 1, 1, 2, 2, 2, 9, 37, 61, 123, 123, 123, 123, 123, 1, 1, 3, 3, 3, 1, 9, 37, 37, 61, 61, 1] 201 rigid atoms, others: [2, 4, 5, 6, 7, 19, 20, 24, 30] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 25, 26, 27, 28, 29]) total number of confs: 383 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567821 none COC(=O)C1=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=CS1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 14, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 6, 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, 123, 201, 123, 123, 69, 47, 69, 69, 18, 8, 1, 1, 1, 1, 1, 1, 1, 123, 123, 201, 201, 201, 123, 47, 18, 18, 8, 8, 123] 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: 702 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567821 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567821 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567821/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567821 Building REAL300025567822 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567822' /scratch/stefan/7901150/working/building/REAL300025567822 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567822 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567822/0 /scratch/stefan/7901150/working/building/REAL300025567822 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 341) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/341 `/scratch/stefan/7901150/working/3D/341' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CC2=CC(S(=O)(=O)NCCC3=NC(=O)O[N-]3)=CC=C2O1) `REAL300025567822.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567822.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567822/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567822 none CC1(C)CC2=CC(S(=O)(=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', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 14, 11, 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, 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: [1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 55, 92, 201, 201, 201, 201, 201, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1, 1, 9, 55, 55, 92, 92, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 37, 19, 20, 21, 22, 38, 29, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36]) total number of confs: 579 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567822 none CC1(C)CC2=CC(S(=O)(=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', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 14, 11, 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, 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, 201, 201, 201, 201, 201, 118, 84, 118, 118, 24, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 84, 25, 25, 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]) total number of confs: 614 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567822 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567822 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567822/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567822 Building REAL300025567823 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567823' /scratch/stefan/7901150/working/building/REAL300025567823 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567823 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567823/0 /scratch/stefan/7901150/working/building/REAL300025567823 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 342) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/342 `/scratch/stefan/7901150/working/3D/342' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=C(F)C=C1F) `REAL300025567823.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567823.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567823/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567823 none CC1=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=C(F)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 15, 1, 1, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 6, 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, 25, 76, 106, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 2, 2, 2, 1, 25, 76, 76, 106, 106, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 16, 17, 18, 19, 20, 24, 30] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 25, 26, 27, 28, 29]) total number of confs: 636 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567823 none CC1=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=C(F)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 15, 1, 1, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 6, 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, 129, 74, 129, 129, 22, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 188, 201, 201, 201, 201, 201, 74, 22, 22, 8, 8, 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]) total number of confs: 709 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567823 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567823 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567823/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567823 Building REAL300025567824 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567824' /scratch/stefan/7901150/working/building/REAL300025567824 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567824 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567824/0 /scratch/stefan/7901150/working/building/REAL300025567824 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 343) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/343 `/scratch/stefan/7901150/working/3D/343' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2=C(Cl)C=CC3=CC=CC=C32)[N-]O1) `REAL300025567824.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567824.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567824/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567824 none O=C1N=C(CCNS(=O)(=O)C2=C(Cl)C=CC3=CC=CC=C32)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 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: [1, 1, 1, 1, 1, 9, 25, 86, 153, 153, 153, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 9, 9, 25, 25, 86, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 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]) total number of confs: 652 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567824 none O=C1N=C(CCNS(=O)(=O)C2=C(Cl)C=CC3=CC=CC=C32)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 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: [201, 201, 201, 97, 59, 19, 9, 1, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 97, 97, 59, 59, 19, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 596 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567824 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567824 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567824/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567824 Building REAL300025567825 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567825' /scratch/stefan/7901150/working/building/REAL300025567825 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567825 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567825/0 /scratch/stefan/7901150/working/building/REAL300025567825 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 344) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/344 `/scratch/stefan/7901150/working/3D/344' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC(C)=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)S1) `REAL300025567825.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567825.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567825/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567825 none CC1=NC(C)=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 1, 8, 1, 5, 1, 14, 11, 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, 6, 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, 8, 8, 8, 16, 58, 93, 201, 201, 201, 201, 201, 1, 2, 2, 2, 2, 2, 2, 16, 58, 58, 93, 93] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 18] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 604 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567825 none CC1=NC(C)=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 1, 8, 1, 5, 1, 14, 11, 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, 6, 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, 177, 95, 177, 177, 24, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 95, 24, 25, 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: 720 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567825 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567825 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567825/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567825 Building REAL300025567826 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567826' /scratch/stefan/7901150/working/building/REAL300025567826 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567826 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567826/0 /scratch/stefan/7901150/working/building/REAL300025567826 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 345) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/345 `/scratch/stefan/7901150/working/3D/345' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CCC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1) `REAL300025567826.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567826/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567826 none N#CCC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 2, 2, 2, 9, 41, 62, 173, 173, 173, 173, 173, 1, 1, 4, 4, 1, 1, 9, 41, 41, 62, 62, 1, 1] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 19, 20, 23, 24, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 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 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567826 none N#CCC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 126, 126, 173, 173, 126, 88, 126, 126, 23, 8, 1, 1, 1, 1, 1, 1, 1, 173, 173, 201, 201, 173, 173, 88, 23, 23, 8, 8, 173, 173] 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: 1097 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567826 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567826 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567826/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567826 Building REAL300025567827 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567827' /scratch/stefan/7901150/working/building/REAL300025567827 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567827 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567827/0 /scratch/stefan/7901150/working/building/REAL300025567827 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 346) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/346 `/scratch/stefan/7901150/working/3D/346' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=CC=C1Br) `REAL300025567827.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567827.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567827/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567827 none COC1=CC(S(=O)(=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', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 14, 11, 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, 6, 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, 3, 3, 3, 9, 40, 69, 172, 172, 172, 172, 172, 1, 1, 1, 1, 4, 4, 4, 1, 9, 40, 40, 69, 69, 1, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 17, 18, 19, 20, 24, 30, 31] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 25, 26, 27, 28, 29]) total number of confs: 474 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567827 none COC1=CC(S(=O)(=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', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 14, 11, 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, 6, 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, 172, 172, 172, 117, 75, 117, 117, 22, 8, 1, 1, 1, 1, 1, 1, 1, 172, 172, 172, 172, 201, 201, 201, 172, 75, 22, 22, 8, 8, 172, 172] 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]) total number of confs: 610 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567827 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567827 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567827/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567827 Building REAL300025567828 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567828' /scratch/stefan/7901150/working/building/REAL300025567828 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567828 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567828/0 /scratch/stefan/7901150/working/building/REAL300025567828 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 347) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/347 `/scratch/stefan/7901150/working/3D/347' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(Br)C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=C1) `REAL300025567828.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567828.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567828/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567828 none COC1=CC=C(Br)C(S(=O)(=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', 'Br', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 17, 1, 14, 11, 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, 7, 7, 7, 6, 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, 3, 3, 3, 5, 30, 58, 199, 199, 199, 199, 199, 1, 3, 3, 3, 1, 1, 5, 30, 30, 58, 58, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 20, 24, 25, 31] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 26, 27, 28, 29, 30]) total number of confs: 447 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567828 none COC1=CC=C(Br)C(S(=O)(=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', 'Br', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 17, 1, 14, 11, 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, 7, 7, 7, 6, 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, 199, 199, 199, 199, 199, 199, 199, 112, 199, 199, 24, 8, 1, 1, 1, 1, 1, 1, 1, 199, 201, 201, 201, 199, 199, 112, 24, 25, 8, 8, 199] 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: 779 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567828 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567828 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567828/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567828 Building REAL300025567829 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567829' /scratch/stefan/7901150/working/building/REAL300025567829 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567829 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567829/0 /scratch/stefan/7901150/working/building/REAL300025567829 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 348) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/348 `/scratch/stefan/7901150/working/3D/348' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CC1(CS(=O)(=O)NCCC2=NC(=O)O[N-]2)CC1) `REAL300025567829.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567829.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567829/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567829 none COC(=O)CC1(CS(=O)(=O)NCCC2=NC(=O)O[N-]2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 7, 7, 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, 6, 4, 7, 7, 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 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 1, 1, 1, 3, 3, 3, 3, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 3, 3, 3, 3, 3, 3, 3, 6, 6, 6, 6, 6, 1, 1, 1, 1] 6 rigid atoms, others: [33, 34, 35, 4, 5, 6, 19, 20, 36] set([0, 1, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 29 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567829 none COC(=O)CC1(CS(=O)(=O)NCCC2=NC(=O)O[N-]2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 7, 7, 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, 6, 4, 7, 7, 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 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 4, 4, 4, 4, 4, 2, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 4, 4, 2, 2, 6, 6, 6, 6] 6 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: 28 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567829 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567829 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567829/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567829 Building REAL300025567830 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567830' /scratch/stefan/7901150/working/building/REAL300025567830 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567830 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567830/0 /scratch/stefan/7901150/working/building/REAL300025567830 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 349) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/349 `/scratch/stefan/7901150/working/3D/349' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC([N+](=O)[O-])=CC(C)=C1S(=O)(=O)NCCC1=NC(=O)O[N-]1) `REAL300025567830.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567830.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567830/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567830 none CC1=CC([N+](=O)[O-])=CC(C)=C1S(=O)(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.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, 8, 11, 11, 1, 1, 5, 1, 14, 11, 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, 3, 3, 7, 7, 7, 7, 7, 6, 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 104 conformations in input total number of sets (complete confs): 104 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 3, 3, 3, 5, 25, 42, 104, 104, 104, 104, 104, 2, 2, 2, 1, 1, 2, 2, 2, 5, 25, 25, 42, 42] 104 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 11, 26, 27] set([5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 298 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567830 none CC1=CC([N+](=O)[O-])=CC(C)=C1S(=O)(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.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, 8, 11, 11, 1, 1, 5, 1, 14, 11, 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, 3, 3, 7, 7, 7, 7, 7, 6, 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 58 conformations in input total number of sets (complete confs): 58 using faster count positions algorithm for large data unique positions, atoms: [58, 58, 58, 58, 58, 58, 58, 58, 58, 58, 58, 56, 58, 58, 21, 8, 1, 1, 1, 1, 1, 1, 1, 58, 58, 58, 58, 58, 58, 58, 58, 56, 21, 21, 8, 8] 58 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: 200 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567830 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567830 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567830/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567830 Building REAL300025567831 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567831' /scratch/stefan/7901150/working/building/REAL300025567831 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567831 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567831/0 /scratch/stefan/7901150/working/building/REAL300025567831 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 350) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/350 `/scratch/stefan/7901150/working/3D/350' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)N1CCN(S(=O)(=O)NCCC2=NC(=O)O[N-]2)CC1) `REAL300025567831.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567831.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567831/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567831 none CS(=O)(=O)N1CCN(S(=O)(=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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [5, 14, 11, 11, 8, 5, 5, 8, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 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, 6, 6, 4, 7, 7, 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, 5, 5, 1, 1, 1, 1, 1, 6, 6, 6, 21, 71, 90, 187, 187, 187, 187, 187, 1, 1, 6, 6, 6, 1, 1, 1, 1, 21, 71, 71, 90, 90, 1, 1, 1, 1] 201 rigid atoms, others: [1, 34, 35, 4, 5, 6, 7, 8, 20, 21, 25, 26, 27, 28, 37, 36] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 29, 30, 31, 32, 33]) total number of confs: 566 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567831 none CS(=O)(=O)N1CCN(S(=O)(=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', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [5, 14, 11, 11, 8, 5, 5, 8, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 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, 6, 6, 4, 7, 7, 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, 187, 201, 201, 187, 187, 187, 131, 80, 131, 131, 24, 8, 1, 1, 1, 1, 1, 1, 1, 187, 187, 201, 201, 201, 187, 187, 187, 187, 80, 24, 24, 8, 8, 187, 187, 187, 187] 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: 696 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567831 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567831 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567831/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567831 Building REAL300025567832 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567832' /scratch/stefan/7901150/working/building/REAL300025567832 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567832 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567832/0 /scratch/stefan/7901150/working/building/REAL300025567832 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 351) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/351 `/scratch/stefan/7901150/working/3D/351' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=CC=C1F) `REAL300025567832.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567832.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567832/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567832 none COC(=O)C1=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=CC=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 12, 1, 11, 1, 1, 1, 14, 11, 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, 3, 7, 5, 7, 7, 7, 7, 6, 6, 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, 1, 8, 1, 1, 1, 1, 2, 2, 2, 9, 31, 47, 120, 120, 120, 120, 120, 1, 1, 1, 1, 8, 8, 8, 1, 9, 31, 31, 47, 47, 1, 1] 201 rigid atoms, others: [32, 33, 2, 4, 5, 6, 7, 19, 20, 21, 22, 26] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 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 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567832 none COC(=O)C1=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=CC=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 12, 1, 11, 1, 1, 1, 14, 11, 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, 3, 7, 5, 7, 7, 7, 7, 6, 6, 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, 120, 201, 120, 120, 74, 49, 74, 74, 20, 8, 1, 1, 1, 1, 1, 1, 1, 120, 120, 120, 120, 201, 201, 201, 120, 49, 20, 20, 8, 8, 120, 120] 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: 722 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567832 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567832 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567832/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567832 Building REAL300025567833 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567833' /scratch/stefan/7901150/working/building/REAL300025567833 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567833 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567833/0 /scratch/stefan/7901150/working/building/REAL300025567833 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 352) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/352 `/scratch/stefan/7901150/working/3D/352' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=C(Cl)C=C1Cl) `REAL300025567833.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567833.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567833/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567833 none COC(=O)C1=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=C(Cl)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 16, 1, 1, 16, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 6, 6, 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, 5, 1, 5, 1, 1, 1, 1, 3, 3, 3, 5, 27, 47, 142, 142, 142, 142, 142, 1, 1, 1, 1, 1, 5, 5, 5, 1, 5, 27, 27, 47, 47, 1] 201 rigid atoms, others: [33, 2, 4, 5, 6, 7, 19, 20, 21, 22, 23, 27] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 28, 29, 30, 31, 32]) total number of confs: 349 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567833 none COC(=O)C1=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=C(Cl)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 16, 1, 1, 16, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 6, 6, 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, 142, 201, 142, 142, 142, 88, 142, 142, 22, 8, 1, 1, 1, 1, 1, 1, 1, 142, 142, 142, 142, 142, 201, 201, 201, 142, 88, 23, 22, 8, 8, 142] 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: 774 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567833 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567833 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567833/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567833 Building REAL300025567834 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567834' /scratch/stefan/7901150/working/building/REAL300025567834 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567834 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567834/0 /scratch/stefan/7901150/working/building/REAL300025567834 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 353) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/353 `/scratch/stefan/7901150/working/3D/353' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C(OC)C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=C1) `REAL300025567834.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567834.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567834/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567834 none COC(=O)C1=CC=C(OC)C(S(=O)(=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', 'C.ar', 'O.3', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 11, 1, 1, 1, 1, 12, 5, 1, 14, 11, 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, 5, 7, 7, 7, 7, 3, 7, 7, 7, 6, 6, 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, 1, 10, 1, 1, 1, 1, 1, 3, 1, 1, 7, 7, 7, 17, 53, 53, 135, 135, 135, 135, 135, 1, 10, 10, 10, 1, 1, 3, 3, 3, 17, 53, 53, 53, 53, 1] 201 rigid atoms, others: [2, 4, 5, 6, 7, 8, 10, 11, 23, 27, 28, 37] set([0, 1, 3, 9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 336 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567834 none COC(=O)C1=CC=C(OC)C(S(=O)(=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', 'C.ar', 'O.3', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 11, 1, 1, 1, 1, 12, 5, 1, 14, 11, 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, 5, 7, 7, 7, 7, 3, 7, 7, 7, 6, 6, 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, 135, 201, 135, 135, 135, 135, 135, 149, 84, 47, 84, 84, 8, 8, 1, 1, 1, 1, 1, 1, 1, 135, 201, 201, 201, 135, 135, 149, 149, 149, 47, 8, 8, 8, 8, 135] 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: 680 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567834 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567834 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567834/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567834 Building REAL300025567835 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567835' /scratch/stefan/7901150/working/building/REAL300025567835 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567835 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567835/0 /scratch/stefan/7901150/working/building/REAL300025567835 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 354) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/354 `/scratch/stefan/7901150/working/3D/354' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(C)=C(C)C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=C1) `REAL300025567835.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567835/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567835 none COC(=O)C1=CC(C)=C(C)C(S(=O)(=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', 'C.3', 'C.ar', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 11, 1, 1, 1, 5, 1, 5, 1, 14, 11, 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, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 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, 1, 13, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 25, 43, 120, 120, 120, 120, 120, 1, 13, 13, 13, 1, 2, 2, 2, 2, 2, 2, 5, 25, 25, 43, 43, 1] 201 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 11, 23, 39, 27] set([0, 1, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 339 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567835 none COC(=O)C1=CC(C)=C(C)C(S(=O)(=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', 'C.3', 'C.ar', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 11, 1, 1, 1, 5, 1, 5, 1, 14, 11, 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, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 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, 120, 201, 120, 120, 120, 120, 116, 120, 120, 80, 120, 120, 24, 8, 1, 1, 1, 1, 1, 1, 1, 120, 201, 201, 201, 120, 120, 120, 120, 120, 120, 120, 80, 24, 24, 8, 8, 120] 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: 783 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567835 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567835 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567835/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567835 Building REAL300025567836 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567836' /scratch/stefan/7901150/working/building/REAL300025567836 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567836 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567836/0 /scratch/stefan/7901150/working/building/REAL300025567836 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 355) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/355 `/scratch/stefan/7901150/working/3D/355' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CC1(CS(=O)(=O)NCCC2=NC(=O)O[N-]2)CC1) `REAL300025567836.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567836.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567836/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567836 none COC(=O)CC1(CS(=O)(=O)NCCC2=NC(=O)O[N-]2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 7, 7, 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, 6, 4, 7, 7, 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 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 1, 1, 1, 3, 3, 3, 3, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 3, 3, 3, 3, 3, 3, 3, 6, 6, 6, 6, 6, 1, 1, 1, 1] 6 rigid atoms, others: [33, 34, 35, 4, 5, 6, 19, 20, 36] set([0, 1, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 29 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567836 none COC(=O)CC1(CS(=O)(=O)NCCC2=NC(=O)O[N-]2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 7, 7, 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, 6, 4, 7, 7, 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 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 4, 4, 4, 4, 4, 2, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 4, 4, 2, 2, 6, 6, 6, 6] 6 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: 28 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567836 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567836 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567836/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567836 Building REAL300025567837 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567837' /scratch/stefan/7901150/working/building/REAL300025567837 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567837 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567837/0 /scratch/stefan/7901150/working/building/REAL300025567837 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 356) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/356 `/scratch/stefan/7901150/working/3D/356' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(Br)SC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=C1) `REAL300025567837.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567837.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567837/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567837 none CC1=C(Br)SC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [5, 1, 1, 17, 14, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 6, 6, 23, 82, 112, 201, 201, 201, 201, 201, 1, 2, 2, 2, 23, 82, 82, 112, 112, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 18, 27] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 641 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567837 none CC1=C(Br)SC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [5, 1, 1, 17, 14, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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, 134, 81, 134, 134, 24, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 81, 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]) total number of confs: 643 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567837 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567837 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567837/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567837 Building REAL300025567838 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567838' /scratch/stefan/7901150/working/building/REAL300025567838 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567838 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567838/0 /scratch/stefan/7901150/working/building/REAL300025567838 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 357) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/357 `/scratch/stefan/7901150/working/3D/357' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCS(=O)(=O)NCCS(=O)(=O)NCCC1=NC(=O)O[N-]1) `REAL300025567838.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567838.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567838/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567838 none CCS(=O)(=O)NCCS(=O)(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', '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, 14, 11, 11, 8, 5, 5, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 6, 4, 7, 7, 7, 6, 6, 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, 172, 142, 172, 172, 79, 79, 59, 39, 59, 59, 8, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 142, 79, 79, 79, 79, 39, 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, 30, 31, 32, 33, 34]) total number of confs: 890 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567838 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567838 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567838/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567838 Building REAL300025567839 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567839' /scratch/stefan/7901150/working/building/REAL300025567839 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567839 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567839/0 /scratch/stefan/7901150/working/building/REAL300025567839 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 358) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/358 `/scratch/stefan/7901150/working/3D/358' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2=CC3=CC(Cl)=CC=C3S2)[N-]O1) `REAL300025567839.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567839.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567839/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567839 none O=C1N=C(CCNS(=O)(=O)C2=CC3=CC(Cl)=CC=C3S2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 16, 1, 1, 1, 14, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 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: [1, 1, 1, 1, 1, 9, 25, 66, 107, 107, 107, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 9, 9, 25, 25, 66, 201, 201, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 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]) total number of confs: 574 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567839 none O=C1N=C(CCNS(=O)(=O)C2=CC3=CC(Cl)=CC=C3S2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 16, 1, 1, 1, 14, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 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: [201, 201, 201, 108, 73, 23, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 108, 108, 73, 73, 23, 1, 1, 1, 1] 201 rigid atoms, others: [7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 640 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567839 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567839 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567839/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567839 Building REAL300025567840 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567840' /scratch/stefan/7901150/working/building/REAL300025567840 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567840 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567840/0 /scratch/stefan/7901150/working/building/REAL300025567840 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 359) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/359 `/scratch/stefan/7901150/working/3D/359' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(F)=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=C1) `REAL300025567840.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567840.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567840/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567840 none CC1=CC(F)=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 1, 1, 1, 15, 1, 1, 14, 11, 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, 7, 7, 7, 7, 7, 7, 7, 6, 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, 1, 2, 2, 2, 9, 51, 89, 201, 201, 201, 201, 201, 1, 2, 2, 2, 1, 1, 9, 51, 51, 89, 89, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 19, 23, 24, 30] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 25, 26, 27, 28, 29]) total number of confs: 565 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567840 none CC1=CC(F)=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 1, 1, 1, 15, 1, 1, 14, 11, 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, 7, 7, 7, 7, 7, 7, 7, 6, 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, 119, 79, 119, 119, 24, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 79, 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]) total number of confs: 649 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567840 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567840 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567840/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567840 Building REAL300025567841 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567841' /scratch/stefan/7901150/working/building/REAL300025567841 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567841 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567841/0 /scratch/stefan/7901150/working/building/REAL300025567841 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 360) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/360 `/scratch/stefan/7901150/working/3D/360' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C(F)(F)F)C=C1S(=O)(=O)NCCC1=NC(=O)O[N-]1) `REAL300025567841.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567841.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567841/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567841 none CC1=CC=C(C(F)(F)F)C=C1S(=O)(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.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, 1, 5, 15, 15, 15, 1, 1, 14, 11, 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, 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 188 conformations in input total number of sets (complete confs): 188 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 13, 55, 91, 188, 188, 188, 188, 188, 2, 2, 2, 1, 1, 1, 13, 57, 57, 91, 91] 188 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 26, 27, 28] set([32, 33, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31]) total number of confs: 559 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567841 none CC1=CC=C(C(F)(F)F)C=C1S(=O)(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.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, 1, 5, 15, 15, 15, 1, 1, 14, 11, 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, 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 188 conformations in input total number of sets (complete confs): 188 using faster count positions algorithm for large data unique positions, atoms: [188, 188, 188, 175, 188, 188, 188, 188, 188, 188, 163, 95, 163, 163, 22, 8, 1, 1, 1, 1, 1, 1, 1, 188, 188, 188, 188, 175, 188, 95, 22, 22, 8, 8] 188 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: 726 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567841 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567841 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567841/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567841 Building REAL300025567842 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567842' /scratch/stefan/7901150/working/building/REAL300025567842 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567842 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567842/0 /scratch/stefan/7901150/working/building/REAL300025567842 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 361) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/361 `/scratch/stefan/7901150/working/3D/361' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C)=C(Br)C=C1S(=O)(=O)NCCC1=NC(=O)O[N-]1) `REAL300025567842.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567842.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567842/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567842 none COC1=CC(C)=C(Br)C=C1S(=O)(=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', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.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, 14, 11, 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, 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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 19, 68, 101, 201, 201, 201, 201, 201, 3, 3, 3, 1, 2, 2, 2, 1, 19, 68, 68, 101, 101] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 25, 29] set([0, 11, 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: 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567842 none COC1=CC(C)=C(Br)C=C1S(=O)(=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', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.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, 14, 11, 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, 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, 158, 201, 201, 201, 201, 158, 93, 158, 158, 23, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 93, 24, 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]) total number of confs: 906 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567842 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567842 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567842/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567842 Building REAL300025567843 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567843' /scratch/stefan/7901150/working/building/REAL300025567843 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567843 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567843/0 /scratch/stefan/7901150/working/building/REAL300025567843 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 362) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/362 `/scratch/stefan/7901150/working/3D/362' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2=CC=CC3=CC=CC=C32)[N-]O1) `REAL300025567843.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567843.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567843/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567843 none O=C1N=C(CCNS(=O)(=O)C2=CC=CC3=CC=CC=C32)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 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 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, 9, 25, 80, 133, 133, 133, 135, 135, 135, 135, 135, 135, 135, 135, 135, 1, 1, 9, 9, 25, 25, 80, 135, 135, 135, 135, 135, 135, 135] 135 rigid atoms, others: [0, 1, 2, 3, 4, 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, 32, 33]) total number of confs: 548 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567843 none O=C1N=C(CCNS(=O)(=O)C2=CC=CC3=CC=CC=C32)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 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 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, 58, 31, 7, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 135, 135, 58, 58, 31, 31, 7, 1, 1, 1, 1, 1, 1, 1] 135 rigid atoms, others: [32, 33, 7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 373 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567843 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567843 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567843/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567843 Building REAL300025567844 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567844' /scratch/stefan/7901150/working/building/REAL300025567844 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567844 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567844/0 /scratch/stefan/7901150/working/building/REAL300025567844 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 363) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/363 `/scratch/stefan/7901150/working/3D/363' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2=CN=C3C=CSC3=C2)[N-]O1) `REAL300025567844.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567844.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567844/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567844 none O=C1N=C(CCNS(=O)(=O)C2=CN=C3C=CSC3=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 8, 1, 1, 1, 14, 1, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 3, 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: [1, 1, 1, 1, 1, 9, 25, 82, 115, 115, 115, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 9, 9, 25, 25, 82, 201, 201, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 19, 20] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567844 none O=C1N=C(CCNS(=O)(=O)C2=CN=C3C=CSC3=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 8, 1, 1, 1, 14, 1, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 3, 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: [201, 201, 201, 94, 52, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 94, 94, 52, 52, 9, 1, 1, 1, 1] 201 rigid atoms, others: [7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 583 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567844 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567844 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567844/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567844 Building REAL300025567845 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567845' /scratch/stefan/7901150/working/building/REAL300025567845 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567845 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567845/0 /scratch/stefan/7901150/working/building/REAL300025567845 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 364) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/364 `/scratch/stefan/7901150/working/3D/364' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCCC2=CC=C(S(=O)(=O)NCCC3=NC(=O)O[N-]3)C=C21) `REAL300025567845.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567845.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567845/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567845 none CN1CCCC2=CC=C(S(=O)(=O)NCCC3=NC(=O)O[N-]3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 8, 5, 5, 5, 1, 1, 1, 1, 14, 11, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 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, 2, 2, 2, 9, 55, 92, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 9, 55, 55, 92, 92, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 39, 21, 33, 32, 22, 26, 27, 28, 29, 30, 31] set([34, 35, 36, 37, 38, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25]) total number of confs: 572 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567845 none CN1CCCC2=CC=C(S(=O)(=O)NCCC3=NC(=O)O[N-]3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 8, 5, 5, 5, 1, 1, 1, 1, 14, 11, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 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, 139, 88, 139, 139, 24, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 88, 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, 37, 38, 39]) total number of confs: 678 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567845 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567845 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567845/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567845 Building REAL300025567846 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567846' /scratch/stefan/7901150/working/building/REAL300025567846 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567846 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567846/0 /scratch/stefan/7901150/working/building/REAL300025567846 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 365) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/365 `/scratch/stefan/7901150/working/3D/365' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(Cl)=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1[N+](=O)[O-]) `REAL300025567846.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567846.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567846/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567846 none CC1=CC(Cl)=C(S(=O)(=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', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 14, 11, 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, 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 128 conformations in input total number of sets (complete confs): 128 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 11, 42, 60, 128, 128, 128, 128, 128, 1, 1, 1, 2, 2, 2, 2, 2, 1, 11, 42, 42, 60, 60, 1] 128 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 18, 19, 20, 26] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31]) total number of confs: 382 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567846 none CC1=CC(Cl)=C(S(=O)(=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', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 14, 11, 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, 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 128 conformations in input total number of sets (complete confs): 128 using faster count positions algorithm for large data unique positions, atoms: [128, 128, 128, 128, 128, 118, 84, 118, 118, 24, 8, 1, 1, 1, 1, 1, 1, 1, 128, 128, 128, 128, 128, 128, 128, 128, 128, 84, 24, 24, 8, 8, 128] 128 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: 473 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567846 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567846 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567846/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567846 Building REAL300025567847 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567847' /scratch/stefan/7901150/working/building/REAL300025567847 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567847 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567847/0 /scratch/stefan/7901150/working/building/REAL300025567847 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 366) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/366 `/scratch/stefan/7901150/working/3D/366' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1Cl) `REAL300025567847.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567847.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567847/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567847 none CC(=O)NC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 16, 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, 6, 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, 3, 3, 3, 9, 49, 75, 168, 168, 168, 168, 168, 1, 1, 1, 4, 4, 4, 4, 1, 1, 9, 49, 49, 75, 75, 1] 201 rigid atoms, others: [34, 3, 4, 5, 6, 7, 8, 20, 21, 22, 27, 28] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 29, 30, 31, 32, 33]) total number of confs: 483 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567847 none CC(=O)NC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 16, 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, 6, 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, 168, 168, 168, 168, 104, 73, 104, 104, 24, 8, 1, 1, 1, 1, 1, 1, 1, 168, 168, 168, 201, 201, 201, 201, 168, 168, 73, 24, 24, 8, 8, 168] 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: 679 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567847 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567847 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567847/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567847 Building REAL300025567848 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567848' /scratch/stefan/7901150/working/building/REAL300025567848 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025567848 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567848/0 /scratch/stefan/7901150/working/building/REAL300025567848 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 367) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/367 `/scratch/stefan/7901150/working/3D/367' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)O1) `REAL300025567848.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567848.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567848/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567848 none CCOC(=O)C1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 5, 12, 1, 11, 1, 1, 1, 1, 14, 11, 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, 3, 7, 5, 7, 7, 7, 7, 7, 6, 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: [7, 3, 3, 1, 3, 1, 1, 1, 1, 1, 6, 6, 6, 19, 53, 63, 166, 166, 166, 166, 166, 1, 7, 7, 7, 7, 7, 1, 1, 19, 53, 53, 63, 63] 201 rigid atoms, others: [3, 5, 6, 7, 8, 9, 21, 27, 28] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33]) total number of confs: 435 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567848 none CCOC(=O)C1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 5, 12, 1, 11, 1, 1, 1, 1, 14, 11, 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, 3, 7, 5, 7, 7, 7, 7, 7, 6, 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: [201, 188, 188, 166, 188, 166, 166, 166, 97, 73, 97, 97, 22, 8, 1, 1, 1, 1, 1, 1, 1, 166, 201, 201, 201, 201, 201, 166, 166, 73, 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, 30, 31, 32, 33]) total number of confs: 658 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567848 /scratch/stefan/7901150/working /scratch/stefan/7901150 mkdir: created directory `1' /scratch/stefan/7901150/working/building/REAL300025567848/1 /scratch/stefan/7901150/working/building/REAL300025567848 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 1 (index: 368) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/368 `/scratch/stefan/7901150/working/3D/368' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C1=CC=C(S(=O)(=O)[N-]CCC2=NC(=O)O[N-]2)O1) `REAL300025567848.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025567848.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567848/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567848 none CCOC(=O)C1=CC=C(S(=O)(=O)[N-]CCC2=NC(=O)O[N-]2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', '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'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 3, 3, 7, 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: [17, 7, 5, 1, 5, 1, 1, 1, 1, 1, 6, 6, 6, 25, 63, 63, 156, 156, 156, 156, 156, 1, 17, 17, 17, 17, 17, 1, 1, 63, 63, 63, 63] 201 rigid atoms, others: [3, 5, 6, 7, 8, 9, 21, 27, 28] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 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 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567848 none CCOC(=O)C1=CC=C(S(=O)(=O)[N-]CCC2=NC(=O)O[N-]2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', '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'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 3, 3, 7, 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, 180, 179, 156, 179, 156, 156, 156, 80, 28, 80, 80, 8, 8, 1, 1, 1, 1, 1, 1, 1, 156, 201, 201, 201, 201, 201, 156, 156, 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]) total number of confs: 611 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567848 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567848 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 1: /scratch/stefan/7901150/working/building/REAL300025567848/1.* 0: /scratch/stefan/7901150/working/building/REAL300025567848/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567848 Building REAL300025567849 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567849' /scratch/stefan/7901150/working/building/REAL300025567849 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567849 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567849/0 /scratch/stefan/7901150/working/building/REAL300025567849 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 369) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/369 `/scratch/stefan/7901150/working/3D/369' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2=CC(F)=CC([N+](=O)[O-])=C2)[N-]O1) `REAL300025567849.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567849.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567849/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567849 none O=C1N=C(CCNS(=O)(=O)C2=CC(F)=CC([N+](=O)[O-])=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 15, 1, 1, 8, 11, 11, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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: [1, 1, 1, 1, 1, 9, 25, 94, 129, 129, 129, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 9, 9, 25, 25, 94, 201, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 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]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567849 none O=C1N=C(CCNS(=O)(=O)C2=CC(F)=CC([N+](=O)[O-])=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 15, 1, 1, 8, 11, 11, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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: [201, 201, 201, 84, 49, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 201, 201, 84, 84, 49, 49, 9, 1, 1, 1] 201 rigid atoms, others: [7, 10, 11, 12, 13, 14, 15, 16, 19, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 17, 18, 20, 21, 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 /scratch/stefan/7901150/working/building/REAL300025567849 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567849 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567849/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567849 Building REAL300025567850 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567850' /scratch/stefan/7901150/working/building/REAL300025567850 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567850 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567850/0 /scratch/stefan/7901150/working/building/REAL300025567850 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 370) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/370 `/scratch/stefan/7901150/working/3D/370' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2=CC=CC3=C2CCCC3)[N-]O1) `REAL300025567850.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567850.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567850/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567850 none O=C1N=C(CCNS(=O)(=O)C2=CC=CC3=C2CCCC3)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 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 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, 9, 25, 83, 122, 122, 122, 125, 125, 125, 125, 125, 125, 125, 125, 125, 1, 1, 9, 9, 25, 25, 83, 125, 125, 125, 125, 125, 125, 125, 125, 125, 125, 125] 125 rigid atoms, others: [0, 1, 2, 3, 4, 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, 32, 33, 34, 35, 36, 37]) total number of confs: 474 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567850 none O=C1N=C(CCNS(=O)(=O)C2=CC=CC3=C2CCCC3)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 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 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, 56, 35, 8, 4, 1, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 125, 125, 56, 56, 36, 36, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 125 rigid atoms, others: [7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 350 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567850 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567850 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567850/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567850 Building REAL300025567851 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567851' /scratch/stefan/7901150/working/building/REAL300025567851 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567851 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567851/0 /scratch/stefan/7901150/working/building/REAL300025567851 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 371) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/371 `/scratch/stefan/7901150/working/3D/371' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1C(F)(F)F) `REAL300025567851.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567851.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567851/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567851 none N#CC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1C(F)(F)F NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 5, 15, 15, 15, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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, 3, 3, 3, 9, 55, 87, 201, 201, 201, 201, 201, 1, 1, 1, 2, 2, 2, 1, 1, 9, 55, 55, 87, 87, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 18, 19, 20, 24, 25, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 26, 27, 28, 29, 30]) total number of confs: 560 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567851 none N#CC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1C(F)(F)F NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 5, 15, 15, 15, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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, 130, 90, 130, 130, 24, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 90, 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]) total number of confs: 641 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567851 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567851 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567851/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567851 Building REAL300025567852 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567852' /scratch/stefan/7901150/working/building/REAL300025567852 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567852 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567852/0 /scratch/stefan/7901150/working/building/REAL300025567852 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 372) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/372 `/scratch/stefan/7901150/working/3D/372' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=C(C)OC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=C1) `REAL300025567852.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567852.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567852/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567852 none COC(=O)C1=C(C)OC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', '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, 12, 1, 11, 1, 1, 5, 12, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 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, 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, 4, 1, 1, 1, 1, 1, 1, 6, 6, 6, 25, 68, 86, 160, 160, 160, 160, 160, 1, 5, 4, 4, 2, 2, 2, 25, 68, 68, 86, 86, 1] 201 rigid atoms, others: [33, 2, 4, 5, 6, 7, 8, 9, 21] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 519 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567852 none COC(=O)C1=C(C)OC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', '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, 12, 1, 11, 1, 1, 5, 12, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 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, 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, 160, 201, 160, 160, 160, 160, 85, 59, 85, 85, 20, 8, 1, 1, 1, 1, 1, 1, 1, 158, 201, 201, 201, 160, 160, 160, 59, 20, 20, 8, 8, 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]) total number of confs: 631 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567852 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567852 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567852/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567852 Building REAL300025567853 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567853' /scratch/stefan/7901150/working/building/REAL300025567853 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567853 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567853/0 /scratch/stefan/7901150/working/building/REAL300025567853 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 373) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/373 `/scratch/stefan/7901150/working/3D/373' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2=CC=C3NC(=O)C=CC3=C2)[N-]O1) `REAL300025567853.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567853.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567853/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567853 none O=C1N=C(CCNS(=O)(=O)C2=CC=C3NC(=O)C=CC3=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in 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, 25, 83, 115, 115, 115, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 9, 9, 25, 25, 83, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 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]) total number of confs: 611 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567853 none O=C1N=C(CCNS(=O)(=O)C2=CC=C3NC(=O)C=CC3=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 95, 56, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 95, 95, 56, 56, 9, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 579 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567853 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567853 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567853/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567853 Building REAL300025567854 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567854' /scratch/stefan/7901150/working/building/REAL300025567854 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567854 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567854/0 /scratch/stefan/7901150/working/building/REAL300025567854 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 374) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/374 `/scratch/stefan/7901150/working/3D/374' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(CS(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1C) `REAL300025567854.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567854.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567854/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567854 none CC1=CC=C(CS(=O)(=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', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 14, 11, 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, 6, 6, 4, 7, 7, 7, 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, 6, 16, 16, 16, 42, 99, 119, 201, 201, 201, 201, 201, 1, 1, 1, 2, 2, 2, 1, 1, 6, 6, 42, 99, 99, 119, 119, 1, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 33, 18, 19, 20, 24, 25] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36]) total number of confs: 676 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567854 none CC1=CC=C(CS(=O)(=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', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 14, 11, 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, 6, 6, 4, 7, 7, 7, 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, 183, 201, 201, 101, 82, 56, 82, 82, 19, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 101, 101, 56, 19, 19, 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]) total number of confs: 715 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567854 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567854 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567854/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567854 Building REAL300025567855 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567855' /scratch/stefan/7901150/working/building/REAL300025567855 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567855 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567855/0 /scratch/stefan/7901150/working/building/REAL300025567855 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 375) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/375 `/scratch/stefan/7901150/working/3D/375' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2=CSC3=CC=C(Cl)C=C23)[N-]O1) `REAL300025567855.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567855.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567855/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567855 none O=C1N=C(CCNS(=O)(=O)C2=CSC3=CC=C(Cl)C=C23)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 14, 1, 1, 1, 1, 16, 1, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 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: [1, 1, 1, 1, 1, 9, 25, 85, 144, 144, 144, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 9, 9, 25, 25, 85, 201, 201, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 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]) total number of confs: 657 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567855 none O=C1N=C(CCNS(=O)(=O)C2=CSC3=CC=C(Cl)C=C23)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 14, 1, 1, 1, 1, 16, 1, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 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: [201, 201, 201, 108, 68, 19, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 108, 108, 68, 68, 19, 1, 1, 1, 1] 201 rigid atoms, others: [7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 641 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567855 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567855 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567855/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567855 Building REAL300025567856 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567856' /scratch/stefan/7901150/working/building/REAL300025567856 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567856 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567856/0 /scratch/stefan/7901150/working/building/REAL300025567856 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 376) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/376 `/scratch/stefan/7901150/working/3D/376' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(OC)=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)S1) `REAL300025567856.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567856/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567856 none COC(=O)C1=CC(OC)=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)S1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 12, 1, 11, 1, 1, 1, 12, 5, 1, 14, 11, 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, 3, 7, 5, 7, 7, 7, 3, 7, 7, 7, 6, 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, 4, 1, 1, 1, 1, 3, 1, 1, 13, 13, 13, 29, 69, 69, 153, 153, 153, 153, 153, 1, 5, 5, 5, 1, 3, 3, 3, 29, 69, 69, 69, 69] 201 rigid atoms, others: [2, 4, 5, 6, 7, 9, 10, 22, 26] set([0, 1, 3, 8, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 422 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567856 none COC(=O)C1=CC(OC)=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)S1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 12, 1, 11, 1, 1, 1, 12, 5, 1, 14, 11, 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, 3, 7, 5, 7, 7, 7, 3, 7, 7, 7, 6, 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: [200, 200, 153, 200, 153, 153, 153, 153, 155, 77, 42, 77, 77, 8, 8, 1, 1, 1, 1, 1, 1, 1, 153, 200, 200, 200, 153, 155, 155, 155, 42, 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]) total number of confs: 584 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567856 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567856 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567856/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567856 Building REAL300025567857 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567857' /scratch/stefan/7901150/working/building/REAL300025567857 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567857 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567857/0 /scratch/stefan/7901150/working/building/REAL300025567857 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 377) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/377 `/scratch/stefan/7901150/working/3D/377' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=NC(Cl)=CC=C1S(=O)(=O)NCCC1=NC(=O)O[N-]1) `REAL300025567857.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567857.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567857/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567857 none COC(=O)C1=NC(Cl)=CC=C1S(=O)(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', '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, 11, 1, 8, 1, 16, 1, 1, 1, 14, 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: [7, 3, 7, 5, 7, 3, 7, 7, 7, 7, 7, 7, 6, 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: [7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 11, 45, 73, 147, 147, 147, 147, 147, 7, 7, 7, 1, 1, 11, 47, 47, 73, 73] 201 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 11, 26, 27] set([0, 1, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32]) total number of confs: 468 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567857 none COC(=O)C1=NC(Cl)=CC=C1S(=O)(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', '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, 11, 1, 8, 1, 16, 1, 1, 1, 14, 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: [7, 3, 7, 5, 7, 3, 7, 7, 7, 7, 7, 7, 6, 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, 147, 201, 147, 147, 147, 147, 147, 147, 115, 76, 115, 115, 18, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 147, 147, 76, 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]) total number of confs: 726 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567857 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567857 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567857/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567857 Building REAL300025567858 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567858' /scratch/stefan/7901150/working/building/REAL300025567858 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567858 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567858/0 /scratch/stefan/7901150/working/building/REAL300025567858 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 378) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/378 `/scratch/stefan/7901150/working/3D/378' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(Br)C=CC=C1S(=O)(=O)NCCC1=NC(=O)O[N-]1) `REAL300025567858.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567858.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567858/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567858 none CC1=C(Br)C=CC=C1S(=O)(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.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, 17, 1, 1, 1, 1, 14, 11, 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, 6, 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, 1, 1, 1, 1, 5, 5, 5, 13, 55, 86, 201, 201, 201, 201, 201, 2, 2, 2, 1, 1, 1, 13, 57, 57, 86, 86] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 23, 24, 25] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30]) total number of confs: 539 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567858 none CC1=C(Br)C=CC=C1S(=O)(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.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, 17, 1, 1, 1, 1, 14, 11, 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, 6, 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, 193, 100, 193, 193, 24, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 100, 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]) total number of confs: 754 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567858 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567858 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567858/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567858 Building REAL300025567859 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567859' /scratch/stefan/7901150/working/building/REAL300025567859 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567859 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567859/0 /scratch/stefan/7901150/working/building/REAL300025567859 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 379) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/379 `/scratch/stefan/7901150/working/3D/379' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)C(=O)NC2=CC=C(S(=O)(=O)NCCC3=NC(=O)O[N-]3)C=C21) `REAL300025567859.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567859.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567859/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567859 none CC1(C)C(=O)NC2=CC=C(S(=O)(=O)NCCC3=NC(=O)O[N-]3)C=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.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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: [5, 5, 5, 1, 11, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 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, 6, 4, 7, 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, 1, 1, 1, 1, 1, 2, 2, 2, 9, 57, 91, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1, 1, 9, 57, 57, 91, 91, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 32, 22, 23, 38, 30, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37]) total number of confs: 579 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567859 none CC1(C)C(=O)NC2=CC=C(S(=O)(=O)NCCC3=NC(=O)O[N-]3)C=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.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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: [5, 5, 5, 1, 11, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 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, 6, 4, 7, 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, 201, 201, 201, 119, 82, 119, 119, 24, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 82, 24, 24, 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]) total number of confs: 625 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567859 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567859 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567859/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567859 Building REAL300025567860 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567860' /scratch/stefan/7901150/working/building/REAL300025567860 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567860 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567860/0 /scratch/stefan/7901150/working/building/REAL300025567860 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 380) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/380 `/scratch/stefan/7901150/working/3D/380' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C(Br)S1) `REAL300025567860.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567860.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567860/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567860 none CC1=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C(Br)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 17, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 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 119 conformations in input total number of sets (complete confs): 119 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 3, 3, 5, 27, 45, 119, 119, 119, 119, 119, 1, 1, 1, 1, 2, 2, 2, 5, 27, 27, 45, 45, 1] 119 rigid atoms, others: [0, 1, 2, 3, 15, 16, 17, 18, 27] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 312 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567860 none CC1=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C(Br)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 17, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 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 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, 83, 119, 119, 22, 8, 1, 1, 1, 1, 1, 1, 1, 119, 119, 119, 119, 119, 119, 119, 83, 23, 23, 8, 8, 119] 119 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: 471 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567860 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567860 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567860/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567860 Building REAL300025567861 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567861' /scratch/stefan/7901150/working/building/REAL300025567861 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567861 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567861/0 /scratch/stefan/7901150/working/building/REAL300025567861 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 381) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/381 `/scratch/stefan/7901150/working/3D/381' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2=CC=C(Cl)C3=CC=CC=C32)[N-]O1) `REAL300025567861.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567861.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567861/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567861 none O=C1N=C(CCNS(=O)(=O)C2=CC=C(Cl)C3=CC=CC=C32)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 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 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, 9, 25, 83, 133, 133, 133, 133, 133, 133, 133, 133, 133, 133, 133, 133, 133, 1, 1, 9, 9, 25, 25, 83, 133, 133, 133, 133, 133, 133] 133 rigid atoms, others: [0, 1, 2, 3, 4, 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]) total number of confs: 540 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567861 none O=C1N=C(CCNS(=O)(=O)C2=CC=C(Cl)C3=CC=CC=C32)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 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 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, 55, 29, 7, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 133, 133, 55, 55, 29, 29, 7, 1, 1, 1, 1, 1, 1] 133 rigid atoms, others: [32, 33, 7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 366 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567861 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567861 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567861/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567861 Building REAL300025567862 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567862' /scratch/stefan/7901150/working/building/REAL300025567862 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567862 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567862/0 /scratch/stefan/7901150/working/building/REAL300025567862 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 382) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/382 `/scratch/stefan/7901150/working/3D/382' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=CC(F)=C1F) `REAL300025567862.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567862.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567862/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567862 none COC(=O)C1=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=CC(F)=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 15, 1, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 6, 6, 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: [12, 12, 1, 12, 1, 1, 1, 1, 2, 2, 2, 9, 34, 48, 124, 124, 124, 124, 124, 1, 1, 1, 1, 1, 13, 13, 13, 1, 9, 34, 34, 48, 48, 1] 201 rigid atoms, others: [33, 2, 4, 5, 6, 7, 19, 20, 21, 22, 23, 27] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 28, 29, 30, 31, 32]) total number of confs: 354 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567862 none COC(=O)C1=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=CC(F)=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 15, 1, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 6, 6, 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, 124, 201, 124, 124, 76, 51, 76, 76, 20, 8, 1, 1, 1, 1, 1, 1, 1, 124, 124, 124, 124, 124, 201, 201, 201, 124, 51, 20, 20, 8, 8, 124] 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: 720 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567862 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567862 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567862/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567862 Building REAL300025567863 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567863' /scratch/stefan/7901150/working/building/REAL300025567863 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567863 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567863/0 /scratch/stefan/7901150/working/building/REAL300025567863 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 383) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/383 `/scratch/stefan/7901150/working/3D/383' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)SC2=CC=CC(F)=C21) `REAL300025567863.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567863.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567863/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567863 none CC1=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)SC2=CC=CC(F)=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 14, 1, 1, 1, 1, 1, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 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, 5, 5, 5, 12, 55, 90, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 55, 55, 90, 90, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 33, 32, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 579 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567863 none CC1=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)SC2=CC=CC(F)=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 14, 1, 1, 1, 1, 1, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 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, 169, 94, 169, 169, 24, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 94, 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: 690 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567863 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567863 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567863/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567863 Building REAL300025567864 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567864' /scratch/stefan/7901150/working/building/REAL300025567864 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567864 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567864/0 /scratch/stefan/7901150/working/building/REAL300025567864 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 384) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/384 `/scratch/stefan/7901150/working/3D/384' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1N(C)C) `REAL300025567864.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567864.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567864/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567864 none CC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1N(C)C 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.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'N.pl3', '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, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 185 conformations in input total number of sets (complete confs): 185 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 50, 88, 185, 185, 185, 185, 185, 1, 1, 1, 3, 3, 2, 2, 2, 1, 1, 9, 50, 50, 88, 88, 1, 4, 4, 4, 4, 4, 4] 185 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 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, 33, 34, 35, 36, 37, 38]) total number of confs: 552 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567864 none CC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1N(C)C 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.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'N.pl3', '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, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 185 conformations in input total number of sets (complete confs): 185 using faster count positions algorithm for large data unique positions, atoms: [185, 185, 185, 185, 134, 88, 134, 134, 24, 8, 1, 1, 1, 1, 1, 1, 1, 185, 185, 185, 185, 185, 185, 185, 185, 185, 185, 88, 24, 24, 8, 8, 185, 185, 185, 185, 185, 185, 185] 185 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: 616 number of broken/clashed sets: 16 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567864 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567864 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567864/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567864 Building REAL300025567865 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567865' /scratch/stefan/7901150/working/building/REAL300025567865 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567865 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567865/0 /scratch/stefan/7901150/working/building/REAL300025567865 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 385) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/385 `/scratch/stefan/7901150/working/3D/385' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)SC=C1) `REAL300025567865.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567865.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567865/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567865 none COC1=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)SC=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 14, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 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, 1, 1, 1, 13, 13, 13, 26, 78, 102, 197, 197, 197, 197, 197, 1, 1, 1, 4, 4, 4, 26, 78, 78, 102, 102, 1, 1] 201 rigid atoms, others: [1, 2, 3, 4, 16, 17, 18, 27, 28] set([0, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 615 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567865 none COC1=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)SC=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 14, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 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, 197, 197, 130, 77, 130, 130, 20, 8, 1, 1, 1, 1, 1, 1, 1, 197, 197, 197, 201, 201, 201, 77, 20, 21, 8, 8, 197, 197] 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]) total number of confs: 625 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567865 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567865 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567865/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567865 Building REAL300025567866 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567866' /scratch/stefan/7901150/working/building/REAL300025567866 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567866 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567866/0 /scratch/stefan/7901150/working/building/REAL300025567866 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 386) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/386 `/scratch/stefan/7901150/working/3D/386' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCS(=O)(=O)C1=CC=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=C1) `REAL300025567866.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567866.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567866/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567866 none CCS(=O)(=O)C1=CC=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.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, 5, 14, 11, 11, 1, 1, 1, 1, 1, 14, 11, 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, 3, 3, 7, 7, 7, 7, 7, 7, 6, 6, 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, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 35, 47, 155, 155, 155, 155, 155, 1, 11, 11, 11, 10, 10, 1, 1, 1, 9, 35, 35, 47, 47, 1] 201 rigid atoms, others: [2, 36, 5, 6, 7, 8, 9, 10, 22, 28, 29, 30] set([0, 1, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35]) total number of confs: 391 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567866 none CCS(=O)(=O)C1=CC=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.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, 5, 14, 11, 11, 1, 1, 1, 1, 1, 14, 11, 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, 3, 3, 7, 7, 7, 7, 7, 7, 6, 6, 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, 160, 155, 160, 160, 155, 155, 155, 155, 101, 75, 101, 101, 24, 8, 1, 1, 1, 1, 1, 1, 1, 155, 201, 201, 201, 201, 201, 155, 155, 155, 75, 24, 24, 8, 8, 155] 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: 779 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567866 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567866 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567866/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567866 Building REAL300025567867 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567867' /scratch/stefan/7901150/working/building/REAL300025567867 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567867 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567867/0 /scratch/stefan/7901150/working/building/REAL300025567867 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 387) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/387 `/scratch/stefan/7901150/working/3D/387' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)OC2=CC=C(F)C=C21) `REAL300025567867.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567867.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567867/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567867 none CC1=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)OC2=CC=C(F)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 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, 8, 8, 8, 18, 66, 104, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 18, 66, 66, 104, 104, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 33, 32, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 621 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567867 none CC1=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)OC2=CC=C(F)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 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, 149, 86, 149, 149, 24, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 86, 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: 687 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567867 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567867 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567867/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567867 Building REAL300025567868 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567868' /scratch/stefan/7901150/working/building/REAL300025567868 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025567868 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567868/0 /scratch/stefan/7901150/working/building/REAL300025567868 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 388) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/388 `/scratch/stefan/7901150/working/3D/388' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=C(Br)O1) `REAL300025567868.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567868.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567868/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567868 none COC(=O)C1=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=C(Br)O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'Br', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 17, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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: [6, 6, 1, 6, 1, 1, 1, 1, 7, 7, 7, 19, 52, 62, 128, 128, 128, 128, 128, 1, 1, 1, 6, 6, 6, 1, 19, 52, 52, 62, 62] 201 rigid atoms, others: [2, 4, 5, 6, 7, 19, 20, 21, 25] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 26, 27, 28, 29, 30]) total number of confs: 385 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567868 none COC(=O)C1=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=C(Br)O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'Br', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 17, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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: [201, 201, 128, 201, 128, 128, 91, 61, 91, 91, 22, 8, 1, 1, 1, 1, 1, 1, 1, 128, 128, 128, 201, 201, 201, 128, 61, 22, 22, 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: 712 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567868 /scratch/stefan/7901150/working /scratch/stefan/7901150 mkdir: created directory `1' /scratch/stefan/7901150/working/building/REAL300025567868/1 /scratch/stefan/7901150/working/building/REAL300025567868 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 1 (index: 389) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/389 `/scratch/stefan/7901150/working/3D/389' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(S(=O)(=O)[N-]CCC2=NC(=O)O[N-]2)=C(Br)O1) `REAL300025567868.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025567868.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567868/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567868 none COC(=O)C1=CC(S(=O)(=O)[N-]CCC2=NC(=O)O[N-]2)=C(Br)O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'Br', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 17, 12, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 5, 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, 13, 1, 13, 1, 1, 1, 1, 7, 7, 7, 21, 67, 67, 162, 162, 162, 162, 162, 1, 1, 1, 13, 13, 13, 1, 67, 67, 67, 67] 201 rigid atoms, others: [2, 4, 5, 6, 7, 19, 20, 21, 25] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 26, 27, 28, 29]) total number of confs: 406 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567868 none COC(=O)C1=CC(S(=O)(=O)[N-]CCC2=NC(=O)O[N-]2)=C(Br)O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'Br', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 17, 12, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 5, 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: [201, 201, 162, 201, 162, 162, 98, 39, 98, 98, 8, 8, 1, 1, 1, 1, 1, 1, 1, 162, 162, 162, 201, 201, 201, 162, 8, 8, 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: 588 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567868 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567868 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 1: /scratch/stefan/7901150/working/building/REAL300025567868/1.* 0: /scratch/stefan/7901150/working/building/REAL300025567868/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567868 Building REAL300025567869 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567869' /scratch/stefan/7901150/working/building/REAL300025567869 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567869 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567869/0 /scratch/stefan/7901150/working/building/REAL300025567869 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 390) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/390 `/scratch/stefan/7901150/working/3D/390' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2=CC=CC3=NON=C32)[N-]O1) `REAL300025567869.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567869.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567869/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567869 none O=C1N=C(CCNS(=O)(=O)C2=CC=CC3=NON=C32)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'O.3', 'N.2', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 12, 8, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 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: [1, 1, 1, 1, 1, 9, 25, 81, 137, 137, 137, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 9, 9, 25, 25, 81, 201, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 19, 20] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 653 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567869 none O=C1N=C(CCNS(=O)(=O)C2=CC=CC3=NON=C32)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'O.3', 'N.2', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 12, 8, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 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: [201, 201, 201, 108, 84, 25, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 108, 108, 84, 84, 25, 1, 1, 1] 201 rigid atoms, others: [7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 624 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567869 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567869 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567869/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567869 Building REAL300025567870 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567870' /scratch/stefan/7901150/working/building/REAL300025567870 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567870 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567870/0 /scratch/stefan/7901150/working/building/REAL300025567870 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 391) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/391 `/scratch/stefan/7901150/working/3D/391' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C([N+](=O)[O-])C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=C1C) `REAL300025567870.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567870.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567870/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567870 none CC1=CC=C([N+](=O)[O-])C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 1, 8, 11, 11, 1, 14, 11, 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, 3, 3, 7, 7, 6, 6, 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 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 3, 15, 24, 41, 41, 41, 41, 41, 1, 1, 2, 2, 2, 1, 1, 3, 15, 15, 24, 24, 2, 2, 2] 41 rigid atoms, others: [0, 1, 2, 3, 4, 5, 8, 9, 21, 22, 26, 27] set([6, 7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 150 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567870 none CC1=CC=C([N+](=O)[O-])C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 1, 8, 11, 11, 1, 14, 11, 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, 3, 3, 7, 7, 6, 6, 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 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [41, 41, 41, 41, 41, 41, 41, 41, 41, 39, 41, 41, 17, 7, 1, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41, 41, 41, 41, 39, 17, 17, 7, 7, 41, 41, 41] 41 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: 153 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567870 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567870 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567870/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567870 Building REAL300025567871 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567871' /scratch/stefan/7901150/working/building/REAL300025567871 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567871 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567871/0 /scratch/stefan/7901150/working/building/REAL300025567871 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 392) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/392 `/scratch/stefan/7901150/working/3D/392' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC(C2=CC=C(S(=O)(=O)NCCC3=NC(=O)O[N-]3)S2)=CS1) `REAL300025567871.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567871.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567871/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567871 none CC1=NC(C2=CC=C(S(=O)(=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', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 14, 11, 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, 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, 9, 9, 9, 9, 26, 26, 26, 54, 88, 111, 201, 201, 201, 201, 201, 9, 1, 1, 2, 2, 2, 9, 9, 54, 88, 88, 111, 111, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 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]) total number of confs: 626 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567871 none CC1=NC(C2=CC=C(S(=O)(=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', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 14, 11, 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, 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, 1, 1, 1, 1, 1, 1, 6, 6, 6, 25, 59, 91, 171, 171, 171, 171, 171, 1, 9, 9, 9, 9, 9, 1, 1, 25, 59, 59, 91, 91, 9] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 20, 26, 27] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33]) total number of confs: 555 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567871 none CC1=NC(C2=CC=C(S(=O)(=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', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 14, 11, 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, 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, 171, 171, 171, 171, 93, 49, 93, 93, 18, 8, 1, 1, 1, 1, 1, 1, 1, 171, 201, 201, 201, 201, 201, 171, 171, 49, 19, 18, 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]) total number of confs: 566 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567871 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567871 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567871/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567871 Building REAL300025567872 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567872' /scratch/stefan/7901150/working/building/REAL300025567872 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567872 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567872/0 /scratch/stefan/7901150/working/building/REAL300025567872 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 393) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/393 `/scratch/stefan/7901150/working/3D/393' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC1=NC=C(Cl)C=C1S(=O)(=O)NCCC1=NC(=O)O[N-]1) `REAL300025567872.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567872.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567872/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567872 none NC1=NC=C(Cl)C=C1S(=O)(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.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: [8, 1, 8, 1, 1, 16, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 6, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [4, 7, 3, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 21, 65, 94, 201, 201, 201, 201, 201, 2, 2, 1, 1, 21, 65, 65, 94, 94] 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: 588 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567872 none NC1=NC=C(Cl)C=C1S(=O)(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.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: [8, 1, 8, 1, 1, 16, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 6, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [4, 7, 3, 7, 7, 7, 7, 7, 7, 6, 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, 123, 71, 123, 123, 22, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 71, 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]) total number of confs: 621 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567872 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567872 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567872/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567872 Building REAL300025567873 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567873' /scratch/stefan/7901150/working/building/REAL300025567873 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567873 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567873/0 /scratch/stefan/7901150/working/building/REAL300025567873 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 394) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/394 `/scratch/stefan/7901150/working/3D/394' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)CC2=CC=C(F)C(Cl)=C2)[N-]O1) `REAL300025567873.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567873.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567873/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567873 none O=C1N=C(CCNS(=O)(=O)CC2=CC=C(F)C(Cl)=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 5, 1, 1, 1, 1, 15, 1, 16, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 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: [1, 1, 1, 1, 1, 8, 22, 67, 90, 90, 90, 119, 200, 201, 201, 201, 201, 201, 200, 1, 1, 8, 8, 22, 22, 67, 119, 119, 201, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 19, 20] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 673 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567873 none O=C1N=C(CCNS(=O)(=O)CC2=CC=C(F)C(Cl)=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 5, 1, 1, 1, 1, 15, 1, 16, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 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: [201, 201, 201, 119, 98, 41, 14, 6, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 119, 119, 98, 98, 41, 6, 6, 1, 1, 1] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 664 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567873 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567873 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567873/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567873 Building REAL300025567874 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567874' /scratch/stefan/7901150/working/building/REAL300025567874 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567874 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567874/0 /scratch/stefan/7901150/working/building/REAL300025567874 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 395) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/395 `/scratch/stefan/7901150/working/3D/395' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCS(=O)(=O)NCCC1=NC(=O)O[N-]1)OCC1=CC=CC=C1) `REAL300025567874.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567874.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567874/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567874 none O=C(CCS(=O)(=O)NCCC1=NC(=O)O[N-]1)OCC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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'] dock atom type numbers: [11, 1, 5, 5, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 6, 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, 7] 0 hydrogens need rotated 8 conformations in input total number of sets (complete confs): 8 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 6, 5, 6, 6, 5, 3, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 5, 5, 3, 3, 8, 8, 8, 8, 8, 8, 8] 8 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: 37 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567874 none O=C(CCS(=O)(=O)NCCC1=NC(=O)O[N-]1)OCC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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'] dock atom type numbers: [11, 1, 5, 5, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 6, 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, 7] 0 hydrogens need rotated 8 conformations in input total number of sets (complete confs): 8 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 3, 3, 3, 3, 3, 7, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 7, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1] 8 rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 33, 39, 34, 16, 17, 18, 19, 20, 21, 22, 23] set([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: 28 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567874 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567874 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567874/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567874 Building REAL300025567875 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567875' /scratch/stefan/7901150/working/building/REAL300025567875 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567875 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567875/0 /scratch/stefan/7901150/working/building/REAL300025567875 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 396) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/396 `/scratch/stefan/7901150/working/3D/396' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2=CN=C3NC(=O)NC(=O)C3=C2)[N-]O1) `REAL300025567875.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567875.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567875/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567875 none O=C1N=C(CCNS(=O)(=O)C2=CN=C3NC(=O)NC(=O)C3=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 8, 1, 8, 1, 11, 8, 1, 11, 1, 1, 8, 12, 7, 7, 7, 7, 6, 7, 6, 6, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 3, 7, 4, 7, 6, 4, 7, 6, 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: [1, 1, 1, 1, 1, 9, 25, 92, 139, 139, 139, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 9, 9, 25, 25, 92, 201, 201, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 22, 23] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 676 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567875 none O=C1N=C(CCNS(=O)(=O)C2=CN=C3NC(=O)NC(=O)C3=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 8, 1, 8, 1, 11, 8, 1, 11, 1, 1, 8, 12, 7, 7, 7, 7, 6, 7, 6, 6, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 3, 7, 4, 7, 6, 4, 7, 6, 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: [201, 201, 201, 87, 53, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 87, 87, 53, 53, 9, 1, 1, 1, 1] 201 rigid atoms, others: [32, 7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 545 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567875 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567875 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567875/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567875 Building REAL300025567876 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567876' /scratch/stefan/7901150/working/building/REAL300025567876 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567876 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567876/0 /scratch/stefan/7901150/working/building/REAL300025567876 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 397) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/397 `/scratch/stefan/7901150/working/3D/397' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C(=O)C1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1) `REAL300025567876.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567876.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567876/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567876 none CC(C)(C)C(=O)C1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.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, 1, 11, 1, 1, 1, 1, 14, 11, 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, 6, 6, 4, 7, 7, 7, 7, 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: [5, 3, 5, 5, 1, 3, 1, 1, 1, 1, 1, 2, 2, 2, 7, 35, 57, 138, 138, 138, 138, 138, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 7, 35, 35, 57, 57, 1, 1] 201 rigid atoms, others: [33, 34, 4, 6, 7, 8, 9, 10, 40, 41, 22, 23] set([0, 1, 2, 3, 5, 11, 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: 389 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567876 none CC(C)(C)C(=O)C1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.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, 1, 11, 1, 1, 1, 1, 14, 11, 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, 6, 6, 4, 7, 7, 7, 7, 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, 146, 201, 201, 112, 146, 112, 138, 138, 112, 73, 112, 112, 24, 8, 1, 1, 1, 1, 1, 1, 1, 138, 138, 201, 201, 201, 201, 201, 201, 201, 201, 201, 138, 138, 73, 25, 25, 8, 8, 138, 138] 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: 1040 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567876 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567876 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567876/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567876 Building REAL300025567877 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567877' /scratch/stefan/7901150/working/building/REAL300025567877 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025567877 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567877/0 /scratch/stefan/7901150/working/building/REAL300025567877 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 398) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/398 `/scratch/stefan/7901150/working/3D/398' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2=CC3=CC=CC=C3O2)[N-]O1) `REAL300025567877.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567877.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567877/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567877 none O=C1N=C(CCNS(=O)(=O)C2=CC3=CC=CC=C3O2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 12, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [1, 1, 1, 1, 1, 9, 25, 83, 147, 147, 147, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 9, 9, 25, 25, 83, 201, 201, 201, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 19, 20] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 696 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567877 none O=C1N=C(CCNS(=O)(=O)C2=CC3=CC=CC=C3O2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 12, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 201, 201, 99, 68, 21, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 99, 99, 68, 68, 21, 1, 1, 1, 1, 1] 201 rigid atoms, others: [7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 604 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567877 /scratch/stefan/7901150/working /scratch/stefan/7901150 mkdir: created directory `1' /scratch/stefan/7901150/working/building/REAL300025567877/1 /scratch/stefan/7901150/working/building/REAL300025567877 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 1 (index: 399) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/399 `/scratch/stefan/7901150/working/3D/399' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CC[N-]S(=O)(=O)C2=CC3=CC=CC=C3O2)[N-]O1) `REAL300025567877.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025567877.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567877/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567877 none O=C1N=C(CC[N-]S(=O)(=O)C2=CC3=CC=CC=C3O2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 12, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 7, 7, 3, 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 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, 9, 13, 45, 101, 101, 101, 135, 135, 135, 135, 135, 135, 135, 135, 1, 1, 9, 9, 13, 13, 135, 135, 135, 135, 135] 135 rigid atoms, others: [0, 1, 2, 3, 4, 19, 20] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 414 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567877 none O=C1N=C(CC[N-]S(=O)(=O)C2=CC3=CC=CC=C3O2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 12, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 7, 7, 3, 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 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, 77, 73, 23, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 135, 135, 77, 77, 73, 73, 1, 1, 1, 1, 1] 135 rigid atoms, others: [7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 19, 20, 21, 22, 23, 24]) total number of confs: 374 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567877 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567877 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 1: /scratch/stefan/7901150/working/building/REAL300025567877/1.* 0: /scratch/stefan/7901150/working/building/REAL300025567877/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567877 Building REAL300025567878 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567878' /scratch/stefan/7901150/working/building/REAL300025567878 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567878 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567878/0 /scratch/stefan/7901150/working/building/REAL300025567878 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 400) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/400 `/scratch/stefan/7901150/working/3D/400' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC2=C(S(=O)(=O)NCCC3=NC(=O)O[N-]3)C=CC=C2C=C1) `REAL300025567878.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567878.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567878/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567878 none CC1=NC2=C(S(=O)(=O)NCCC3=NC(=O)O[N-]3)C=CC=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [5, 1, 8, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 6, 4, 7, 7, 7, 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, 19, 70, 100, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 2, 2, 2, 19, 70, 70, 100, 100, 1, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 35, 32, 34, 17, 18, 19, 20, 21, 22, 33, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 614 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567878 none CC1=NC2=C(S(=O)(=O)NCCC3=NC(=O)O[N-]3)C=CC=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [5, 1, 8, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 6, 4, 7, 7, 7, 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, 155, 83, 155, 155, 20, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 83, 20, 21, 8, 8, 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]) total number of confs: 686 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567878 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567878 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567878/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567878 Building REAL300025567879 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567879' /scratch/stefan/7901150/working/building/REAL300025567879 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567879 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567879/0 /scratch/stefan/7901150/working/building/REAL300025567879 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 401) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/401 `/scratch/stefan/7901150/working/3D/401' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C2=CC(Cl)=CC=C2S1) `REAL300025567879.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567879.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567879/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567879 none CC1=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C2=CC(Cl)=CC=C2S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 16, 1, 1, 1, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 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 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, 7, 7, 7, 10, 45, 76, 153, 153, 153, 153, 153, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 45, 45, 76, 76, 1, 1, 1] 153 rigid atoms, others: [0, 1, 2, 3, 33, 32, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 480 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567879 none CC1=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C2=CC(Cl)=CC=C2S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 16, 1, 1, 1, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 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 153 conformations in input total number of sets (complete confs): 153 using faster count positions algorithm for large data unique positions, atoms: [153, 153, 120, 79, 120, 120, 24, 8, 1, 1, 1, 1, 1, 1, 1, 153, 153, 153, 153, 153, 153, 153, 153, 153, 153, 153, 79, 24, 24, 8, 8, 153, 153, 153] 153 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: 522 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567879 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567879 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567879/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567879 Building REAL300025567880 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567880' /scratch/stefan/7901150/working/building/REAL300025567880 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567880 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567880/0 /scratch/stefan/7901150/working/building/REAL300025567880 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 402) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/402 `/scratch/stefan/7901150/working/3D/402' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=NSC=C1S(=O)(=O)NCCC1=NC(=O)O[N-]1) `REAL300025567880.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567880/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567880 none COC(=O)C1=NSC=C1S(=O)(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'N.2', 'S.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.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, 12, 1, 11, 1, 8, 14, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 6, 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: [11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 11, 45, 83, 169, 169, 169, 169, 169, 11, 11, 11, 1, 11, 47, 47, 83, 83] 201 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 24] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29]) total number of confs: 540 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567880 none COC(=O)C1=NSC=C1S(=O)(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'N.2', 'S.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.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, 12, 1, 11, 1, 8, 14, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 6, 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, 169, 201, 169, 169, 169, 169, 135, 79, 135, 135, 22, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 169, 79, 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: 728 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567880 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567880 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567880/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567880 Building REAL300025567881 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567881' /scratch/stefan/7901150/working/building/REAL300025567881 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567881 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567881/0 /scratch/stefan/7901150/working/building/REAL300025567881 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 403) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/403 `/scratch/stefan/7901150/working/3D/403' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(F)=C([N+](=O)[O-])C=C1S(=O)(=O)NCCC1=NC(=O)O[N-]1) `REAL300025567881.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567881.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567881/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567881 none CC1=CC(F)=C([N+](=O)[O-])C=C1S(=O)(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', '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, 1, 15, 1, 8, 11, 11, 1, 1, 14, 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: [7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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, 2, 2, 1, 1, 1, 5, 5, 5, 11, 48, 76, 165, 165, 165, 165, 165, 2, 2, 2, 1, 1, 11, 50, 50, 76, 76] 165 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 9, 10, 11, 26, 27] set([32, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31]) total number of confs: 479 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567881 none CC1=CC(F)=C([N+](=O)[O-])C=C1S(=O)(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', '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, 1, 15, 1, 8, 11, 11, 1, 1, 14, 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: [7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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, 161, 107, 161, 161, 24, 8, 1, 1, 1, 1, 1, 1, 1, 165, 165, 165, 165, 165, 107, 24, 24, 8, 8] 165 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: 595 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567881 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567881 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567881/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567881 Building REAL300025567882 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567882' /scratch/stefan/7901150/working/building/REAL300025567882 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567882 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567882/0 /scratch/stefan/7901150/working/building/REAL300025567882 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 404) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/404 `/scratch/stefan/7901150/working/3D/404' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)CCC2=CC=CC=C2[N+](=O)[O-])[N-]O1) `REAL300025567882.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567882.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567882/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567882 none O=C1N=C(CCNS(=O)(=O)CCC2=CC=CC=C2[N+](=O)[O-])[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 5, 5, 1, 1, 1, 1, 1, 1, 8, 11, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [1, 1, 1, 1, 1, 9, 25, 94, 134, 134, 134, 184, 184, 201, 201, 184, 201, 201, 201, 201, 201, 1, 1, 9, 9, 25, 25, 94, 184, 184, 184, 184, 201, 201, 184, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 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, 35]) total number of confs: 839 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567882 none O=C1N=C(CCNS(=O)(=O)CCC2=CC=CC=C2[N+](=O)[O-])[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 5, 5, 1, 1, 1, 1, 1, 1, 8, 11, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [201, 201, 201, 117, 94, 38, 18, 4, 18, 18, 4, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 201, 201, 117, 117, 94, 94, 38, 4, 4, 4, 4, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 656 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567882 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567882 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567882/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567882 Building REAL300025567883 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567883' /scratch/stefan/7901150/working/building/REAL300025567883 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567883 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567883/0 /scratch/stefan/7901150/working/building/REAL300025567883 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 405) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/405 `/scratch/stefan/7901150/working/3D/405' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)CCC2=CC=C([N+](=O)[O-])C=C2)[N-]O1) `REAL300025567883.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567883.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567883/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567883 none O=C1N=C(CCNS(=O)(=O)CCC2=CC=C([N+](=O)[O-])C=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 5, 5, 1, 1, 1, 1, 8, 11, 11, 1, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 3, 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, 9, 25, 88, 129, 129, 129, 185, 187, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 9, 9, 25, 25, 88, 185, 185, 187, 187, 201, 201, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 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, 35]) total number of confs: 822 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567883 none O=C1N=C(CCNS(=O)(=O)CCC2=CC=C([N+](=O)[O-])C=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 5, 5, 1, 1, 1, 1, 8, 11, 11, 1, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 3, 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, 114, 92, 37, 11, 5, 11, 11, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 114, 114, 92, 92, 37, 5, 5, 3, 3, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 631 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567883 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567883 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567883/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567883 Building REAL300025567884 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567884' /scratch/stefan/7901150/working/building/REAL300025567884 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567884 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567884/0 /scratch/stefan/7901150/working/building/REAL300025567884 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 406) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/406 `/scratch/stefan/7901150/working/3D/406' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC(Br)=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=C1) `REAL300025567884.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567884.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567884/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567884 none N#CC1=CC(Br)=CC(S(=O)(=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', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [8, 1, 1, 1, 1, 17, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 3, 3, 3, 9, 49, 85, 201, 201, 201, 201, 201, 1, 1, 1, 9, 49, 49, 85, 85, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 28] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27]) total number of confs: 548 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567884 none N#CC1=CC(Br)=CC(S(=O)(=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', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [8, 1, 1, 1, 1, 17, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 117, 85, 117, 117, 24, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 85, 24, 24, 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]) total number of confs: 621 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567884 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567884 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567884/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567884 Building REAL300025567885 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567885' /scratch/stefan/7901150/working/building/REAL300025567885 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567885 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567885/0 /scratch/stefan/7901150/working/building/REAL300025567885 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 407) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/407 `/scratch/stefan/7901150/working/3D/407' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C1=C(C)C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=C(C)N1) `REAL300025567885.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567885.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567885/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567885 none CCOC(=O)C1=C(C)C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.3', 'N.pl3', '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, 1, 1, 5, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 7, 6, 1, 5, 1, 1, 1, 1, 1, 5, 5, 5, 8, 30, 46, 126, 126, 126, 126, 126, 1, 1, 1, 13, 13, 13, 12, 12, 2, 2, 2, 8, 30, 30, 46, 46, 2, 2, 2, 1] 201 rigid atoms, others: [3, 5, 6, 7, 8, 9, 40, 21, 22, 23] set([0, 1, 2, 4, 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]) total number of confs: 372 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567885 none CCOC(=O)C1=C(C)C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.3', 'N.pl3', '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, 1, 1, 5, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need 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, 184, 126, 184, 126, 126, 126, 112, 57, 112, 112, 16, 8, 1, 1, 1, 1, 1, 1, 1, 126, 126, 126, 201, 201, 201, 201, 201, 126, 126, 126, 57, 16, 17, 8, 8, 126, 126, 126, 126] 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: 766 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567885 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567885 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567885/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567885 Building REAL300025567886 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567886' /scratch/stefan/7901150/working/building/REAL300025567886 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567886 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567886/0 /scratch/stefan/7901150/working/building/REAL300025567886 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 408) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/408 `/scratch/stefan/7901150/working/3D/408' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(F)=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1F) `REAL300025567886.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567886.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567886/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567886 none CC1=CC(F)=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [5, 1, 1, 1, 15, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 23, 67, 101, 201, 199, 201, 201, 201, 1, 1, 1, 2, 2, 2, 1, 23, 67, 67, 101, 101, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 18, 19, 20, 24, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 25, 26, 27, 28, 29]) total number of confs: 624 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567886 none CC1=CC(F)=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [5, 1, 1, 1, 15, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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, 136, 80, 136, 136, 24, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 80, 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]) total number of confs: 657 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567886 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567886 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567886/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567886 Building REAL300025567887 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567887' /scratch/stefan/7901150/working/building/REAL300025567887 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567887 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567887/0 /scratch/stefan/7901150/working/building/REAL300025567887 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 409) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/409 `/scratch/stefan/7901150/working/3D/409' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C1=CC=C(Br)C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=C1) `REAL300025567887.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567887.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567887/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567887 none CN(C)C1=CC=C(Br)C(S(=O)(=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.ar', 'Br', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 17, 1, 14, 11, 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, 6, 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, 3, 3, 3, 5, 28, 55, 193, 193, 193, 193, 193, 1, 6, 6, 6, 6, 6, 6, 1, 1, 5, 28, 28, 55, 55, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 35, 21, 28, 29] set([0, 2, 10, 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: 436 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567887 none CN(C)C1=CC=C(Br)C(S(=O)(=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.ar', 'Br', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 17, 1, 14, 11, 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, 6, 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, 193, 201, 193, 193, 193, 193, 193, 193, 98, 193, 193, 24, 8, 1, 1, 1, 1, 1, 1, 1, 193, 201, 201, 201, 201, 201, 201, 193, 193, 98, 24, 24, 8, 8, 193] 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: 796 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567887 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567887 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567887/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567887 Building REAL300025567888 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567888' /scratch/stefan/7901150/working/building/REAL300025567888 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567888 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567888/0 /scratch/stefan/7901150/working/building/REAL300025567888 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 410) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/410 `/scratch/stefan/7901150/working/3D/410' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN2C=C(S(=O)(=O)NCCC3=NC(=O)O[N-]3)C=NC2=C1Cl) `REAL300025567888.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567888.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567888/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567888 none CC1=NN2C=C(S(=O)(=O)NCCC3=NC(=O)O[N-]3)C=NC2=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'C.2', 'C.2', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 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, 6, 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, 3, 3, 3, 9, 53, 91, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 2, 2, 2, 1, 9, 53, 53, 91, 91, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 18, 19, 20, 21, 22, 26] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 27, 28, 29, 30, 31]) total number of confs: 565 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567888 none CC1=NN2C=C(S(=O)(=O)NCCC3=NC(=O)O[N-]3)C=NC2=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'C.2', 'C.2', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 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, 6, 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, 114, 77, 114, 114, 24, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 77, 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]) total number of confs: 626 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567888 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567888 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567888/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567888 Building REAL300025567889 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567889' /scratch/stefan/7901150/working/building/REAL300025567889 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567889 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567889/0 /scratch/stefan/7901150/working/building/REAL300025567889 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 411) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/411 `/scratch/stefan/7901150/working/3D/411' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=CC=C1Cl) `REAL300025567889.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567889.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567889/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567889 none COC(=O)C1=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=CC=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 16, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 6, 6, 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, 5, 1, 5, 1, 1, 1, 1, 2, 2, 2, 9, 30, 43, 153, 153, 153, 153, 153, 1, 1, 1, 1, 5, 5, 5, 1, 9, 30, 30, 43, 43, 1, 1] 201 rigid atoms, others: [32, 33, 2, 4, 5, 6, 7, 19, 20, 21, 22, 26] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 27, 28, 29, 30, 31]) total number of confs: 346 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567889 none COC(=O)C1=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=CC=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 16, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 6, 6, 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, 153, 201, 153, 153, 90, 60, 90, 90, 18, 8, 1, 1, 1, 1, 1, 1, 1, 153, 153, 153, 153, 201, 201, 201, 153, 60, 18, 18, 8, 8, 153, 153] 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: 691 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567889 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567889 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567889/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567889 Building REAL300025567890 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567890' /scratch/stefan/7901150/working/building/REAL300025567890 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567890 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567890/0 /scratch/stefan/7901150/working/building/REAL300025567890 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 412) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/412 `/scratch/stefan/7901150/working/3D/412' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)CC2=CC(Cl)=CC(Cl)=C2)[N-]O1) `REAL300025567890.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567890/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567890 none O=C1N=C(CCNS(=O)(=O)CC2=CC(Cl)=CC(Cl)=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 5, 1, 1, 1, 16, 1, 1, 16, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 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: [1, 1, 1, 1, 1, 9, 23, 99, 150, 150, 150, 191, 201, 201, 201, 197, 201, 201, 201, 1, 1, 9, 9, 23, 23, 99, 191, 191, 201, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 19, 20] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 840 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567890 none O=C1N=C(CCNS(=O)(=O)CC2=CC(Cl)=CC(Cl)=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 5, 1, 1, 1, 16, 1, 1, 16, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 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: [201, 201, 201, 121, 92, 31, 13, 4, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 121, 121, 92, 92, 31, 4, 4, 1, 1, 1] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 657 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567890 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567890 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567890/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567890 Building REAL300025567891 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567891' /scratch/stefan/7901150/working/building/REAL300025567891 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567891 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567891/0 /scratch/stefan/7901150/working/building/REAL300025567891 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 413) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/413 `/scratch/stefan/7901150/working/3D/413' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=CC=C1[N+](=O)[O-]) `REAL300025567891.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567891.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567891/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567891 none COC1=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=CC=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 8, 11, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 3, 3, 3, 9, 47, 85, 199, 199, 199, 199, 199, 1, 1, 1, 1, 2, 2, 3, 3, 3, 1, 9, 47, 47, 85, 85, 1, 1] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 33, 17, 18, 19, 20, 26] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31]) total number of confs: 556 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567891 none COC1=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=CC=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 8, 11, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 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] 0 hydrogens need 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, 141, 84, 141, 141, 24, 8, 1, 1, 1, 1, 1, 1, 1, 199, 199, 199, 199, 199, 199, 201, 201, 201, 199, 84, 24, 24, 8, 8, 199, 199] 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: 683 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567891 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567891 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567891/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567891 Building REAL300025567892 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567892' /scratch/stefan/7901150/working/building/REAL300025567892 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567892 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567892/0 /scratch/stefan/7901150/working/building/REAL300025567892 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 414) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/414 `/scratch/stefan/7901150/working/3D/414' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(OC)=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=C1) `REAL300025567892.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567892/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567892 none COC1=CC(OC)=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 12, 5, 1, 1, 14, 11, 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, 3, 7, 7, 7, 7, 6, 6, 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, 2, 1, 1, 1, 2, 2, 2, 9, 30, 47, 139, 139, 139, 139, 139, 1, 3, 3, 3, 1, 3, 3, 3, 1, 9, 30, 30, 47, 47, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 7, 8, 9, 35, 21, 25, 29] set([0, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 26, 27, 28, 30, 31, 32, 33, 34]) total number of confs: 331 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567892 none COC1=CC(OC)=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 12, 5, 1, 1, 14, 11, 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, 3, 7, 7, 7, 7, 6, 6, 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, 139, 139, 139, 139, 139, 201, 139, 139, 91, 139, 139, 24, 8, 1, 1, 1, 1, 1, 1, 1, 139, 201, 201, 201, 139, 201, 201, 201, 139, 91, 24, 24, 8, 8, 139] 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: 782 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567892 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567892 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567892/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567892 Building REAL300025567893 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567893' /scratch/stefan/7901150/working/building/REAL300025567893 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025567893 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567893/0 /scratch/stefan/7901150/working/building/REAL300025567893 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 415) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/415 `/scratch/stefan/7901150/working/3D/415' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(Br)SC(S(=O)(=O)[N-]CCC2=NC(=O)O[N-]2)=N1) `REAL300025567893.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567893.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567893/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567893 none CC1=C(Br)SC(S(=O)(=O)[N-]CCC2=NC(=O)O[N-]2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', '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'] dock atom type numbers: [5, 1, 1, 17, 14, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 5, 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: [1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 49, 138, 138, 201, 201, 201, 201, 201, 1, 2, 2, 2, 138, 138, 138, 138] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 18] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 604 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567893 none CC1=C(Br)SC(S(=O)(=O)[N-]CCC2=NC(=O)O[N-]2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', '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'] dock atom type numbers: [5, 1, 1, 17, 14, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 5, 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: [201, 201, 201, 201, 201, 100, 38, 100, 100, 8, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 8, 8, 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]) total number of confs: 496 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567893 /scratch/stefan/7901150/working /scratch/stefan/7901150 mkdir: created directory `1' /scratch/stefan/7901150/working/building/REAL300025567893/1 /scratch/stefan/7901150/working/building/REAL300025567893 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 1 (index: 416) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/416 `/scratch/stefan/7901150/working/3D/416' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(Br)SC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=N1) `REAL300025567893.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025567893.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567893/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567893 none CC1=C(Br)SC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [5, 1, 1, 17, 14, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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, 13, 13, 13, 40, 102, 126, 201, 201, 201, 201, 201, 1, 2, 2, 2, 40, 102, 102, 126, 126] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 18] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 675 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567893 none CC1=C(Br)SC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [5, 1, 1, 17, 14, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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, 116, 68, 116, 116, 19, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 68, 20, 20, 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: 601 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567893 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567893 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 1: /scratch/stefan/7901150/working/building/REAL300025567893/1.* 0: /scratch/stefan/7901150/working/building/REAL300025567893/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567893 Building REAL300025567894 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567894' /scratch/stefan/7901150/working/building/REAL300025567894 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567894 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567894/0 /scratch/stefan/7901150/working/building/REAL300025567894 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 417) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/417 `/scratch/stefan/7901150/working/3D/417' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2=CC=C3CCS(=O)(=O)C3=C2)[N-]O1) `REAL300025567894.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567894.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567894/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567894 none O=C1N=C(CCNS(=O)(=O)C2=CC=C3CCS(=O)(=O)C3=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 5, 5, 14, 11, 11, 1, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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: [1, 1, 1, 1, 1, 9, 25, 96, 148, 148, 148, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 9, 9, 25, 25, 96, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 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: 672 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567894 none O=C1N=C(CCNS(=O)(=O)C2=CC=C3CCS(=O)(=O)C3=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 5, 5, 14, 11, 11, 1, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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: [201, 201, 201, 91, 54, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 91, 91, 54, 54, 9, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 565 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567894 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567894 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567894/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567894 Building REAL300025567895 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567895' /scratch/stefan/7901150/working/building/REAL300025567895 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567895 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567895/0 /scratch/stefan/7901150/working/building/REAL300025567895 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 418) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/418 `/scratch/stefan/7901150/working/3D/418' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=C(F)C=CC=C1S(=O)(=O)NCCC1=NC(=O)O[N-]1) `REAL300025567895.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567895.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567895/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567895 none COC(=O)C1=C(F)C=CC=C1S(=O)(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.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, 11, 1, 1, 15, 1, 1, 1, 1, 14, 11, 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, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 11, 40, 62, 136, 136, 136, 136, 136, 7, 7, 7, 1, 1, 1, 11, 42, 42, 62, 62] 201 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 11, 26, 27, 28] set([0, 1, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33]) total number of confs: 412 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567895 none COC(=O)C1=C(F)C=CC=C1S(=O)(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.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, 11, 1, 1, 15, 1, 1, 1, 1, 14, 11, 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, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 136, 201, 136, 136, 136, 136, 136, 136, 101, 65, 101, 101, 19, 9, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 136, 136, 136, 65, 19, 19, 9, 9] 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: 738 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567895 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567895 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567895/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567895 Building REAL300025567896 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567896' /scratch/stefan/7901150/working/building/REAL300025567896 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567896 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567896/0 /scratch/stefan/7901150/working/building/REAL300025567896 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 419) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/419 `/scratch/stefan/7901150/working/3D/419' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CN(C2=CC=C(S(=O)(=O)NCCC3=NC(=O)O[N-]3)C=C2F)N=C1) `REAL300025567896.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567896.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567896/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567896 none CC1=CN(C2=CC=C(S(=O)(=O)NCCC3=NC(=O)O[N-]3)C=C2F)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'F', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 15, 8, 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, 7, 7, 6, 6, 4, 7, 7, 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, 5, 5, 2, 4, 7, 7, 7, 25, 81, 107, 201, 201, 201, 201, 201, 5, 5, 5, 1, 1, 2, 2, 2, 1, 5, 5, 25, 81, 81, 107, 107, 5, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 37, 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]) total number of confs: 607 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567896 none CC1=CN(C2=CC=C(S(=O)(=O)NCCC3=NC(=O)O[N-]3)C=C2F)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'F', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 15, 8, 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, 7, 7, 6, 6, 4, 7, 7, 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, 5, 5, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 47, 79, 159, 159, 159, 159, 159, 1, 1, 1, 5, 5, 5, 5, 5, 5, 1, 1, 9, 47, 47, 79, 79, 1, 5] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 20, 21, 22, 36, 29, 30] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 37]) total number of confs: 482 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567896 none CC1=CN(C2=CC=C(S(=O)(=O)NCCC3=NC(=O)O[N-]3)C=C2F)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'F', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 15, 8, 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, 7, 7, 6, 6, 4, 7, 7, 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, 159, 159, 159, 159, 96, 66, 96, 96, 24, 8, 1, 1, 1, 1, 1, 1, 1, 159, 159, 159, 201, 201, 201, 201, 201, 201, 159, 159, 66, 24, 24, 8, 8, 159, 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]) total number of confs: 591 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567896 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567896 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567896/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567896 Building REAL300025567897 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567897' /scratch/stefan/7901150/working/building/REAL300025567897 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567897 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567897/0 /scratch/stefan/7901150/working/building/REAL300025567897 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 420) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/420 `/scratch/stefan/7901150/working/3D/420' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)CCNS(=O)(=O)C2=CC=CC=C2)[N-]O1) `REAL300025567897.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567897.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567897/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567897 none O=C1N=C(CCNS(=O)(=O)CCNS(=O)(=O)C2=CC=CC=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 4, 7, 6, 6, 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, 9, 9, 29, 42, 42, 42, 71, 71, 146, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 9, 9, 9, 9, 29, 71, 71, 71, 71, 146, 201, 201, 201, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 22, 23] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 832 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567897 none O=C1N=C(CCNS(=O)(=O)CCNS(=O)(=O)C2=CC=CC=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 4, 7, 6, 6, 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: [201, 201, 201, 90, 90, 63, 41, 25, 41, 41, 25, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 90, 90, 90, 90, 63, 25, 25, 25, 25, 5, 1, 1, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 38, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 564 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567897 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567897 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567897/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567897 Building REAL300025567898 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567898' /scratch/stefan/7901150/working/building/REAL300025567898 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025567898 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567898/0 /scratch/stefan/7901150/working/building/REAL300025567898 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 421) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/421 `/scratch/stefan/7901150/working/3D/421' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC(F)=C(S(=O)(=O)[N-]CCC2=NC(=O)O[N-]2)C(F)=C1) `REAL300025567898.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567898.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567898/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567898 none N#CC1=CC(F)=C(S(=O)(=O)[N-]CCC2=NC(=O)O[N-]2)C(F)=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', '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'] dock atom type numbers: [8, 1, 1, 1, 1, 15, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 15, 1, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 5, 3, 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, 9, 9, 9, 19, 57, 61, 132, 132, 132, 132, 132, 1, 1, 1, 1, 57, 57, 61, 61, 1] 132 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 27] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26]) total number of confs: 332 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567898 none N#CC1=CC(F)=C(S(=O)(=O)[N-]CCC2=NC(=O)O[N-]2)C(F)=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', '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'] dock atom type numbers: [8, 1, 1, 1, 1, 15, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 15, 1, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 5, 3, 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, 131, 123, 132, 132, 132, 119, 49, 119, 119, 14, 8, 1, 1, 1, 1, 1, 1, 1, 132, 132, 132, 132, 14, 14, 8, 8, 132] 132 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]) total number of confs: 498 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567898 /scratch/stefan/7901150/working /scratch/stefan/7901150 mkdir: created directory `1' /scratch/stefan/7901150/working/building/REAL300025567898/1 /scratch/stefan/7901150/working/building/REAL300025567898 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 1 (index: 422) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/422 `/scratch/stefan/7901150/working/3D/422' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC(F)=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C(F)=C1) `REAL300025567898.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025567898.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567898/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567898 none N#CC1=CC(F)=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C(F)=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [8, 1, 1, 1, 1, 15, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 15, 1, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 10, 10, 10, 22, 73, 105, 201, 201, 201, 201, 201, 1, 1, 1, 1, 22, 73, 73, 105, 105, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 28] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27]) total number of confs: 608 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567898 none N#CC1=CC(F)=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C(F)=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [8, 1, 1, 1, 1, 15, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 15, 1, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 186, 201, 201, 201, 185, 113, 185, 185, 24, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 113, 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]) total number of confs: 799 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567898 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567898 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 1: /scratch/stefan/7901150/working/building/REAL300025567898/1.* 0: /scratch/stefan/7901150/working/building/REAL300025567898/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567898 Building REAL300025567899 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567899' /scratch/stefan/7901150/working/building/REAL300025567899 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567899 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567899/0 /scratch/stefan/7901150/working/building/REAL300025567899 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 423) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/423 `/scratch/stefan/7901150/working/3D/423' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)CC2=CC=CC=C2[N+](=O)[O-])[N-]O1) `REAL300025567899.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567899.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567899/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567899 none O=C1N=C(CCNS(=O)(=O)CC2=CC=CC=C2[N+](=O)[O-])[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 5, 1, 1, 1, 1, 1, 1, 8, 11, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [1, 1, 1, 1, 1, 8, 22, 82, 133, 133, 133, 188, 201, 201, 192, 201, 201, 201, 201, 201, 1, 1, 8, 8, 22, 22, 82, 188, 188, 201, 201, 188, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 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, 32]) total number of confs: 886 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567899 none O=C1N=C(CCNS(=O)(=O)CC2=CC=CC=C2[N+](=O)[O-])[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 5, 1, 1, 1, 1, 1, 1, 8, 11, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 201, 201, 117, 97, 37, 12, 4, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 201, 201, 117, 117, 97, 97, 37, 4, 4, 1, 1, 1, 1] 201 rigid atoms, others: [32, 10, 11, 12, 13, 14, 15, 16, 17, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 658 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567899 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567899 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567899/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567899 Building REAL300025567900 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567900' /scratch/stefan/7901150/working/building/REAL300025567900 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567900 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567900/0 /scratch/stefan/7901150/working/building/REAL300025567900 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 424) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/424 `/scratch/stefan/7901150/working/3D/424' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2=CC=C(Br)C([N+](=O)[O-])=C2)[N-]O1) `REAL300025567900.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567900.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567900/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567900 none O=C1N=C(CCNS(=O)(=O)C2=CC=C(Br)C([N+](=O)[O-])=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 17, 1, 8, 11, 11, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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: [1, 1, 1, 1, 1, 9, 25, 95, 139, 139, 139, 201, 201, 139, 201, 201, 201, 201, 201, 201, 1, 1, 9, 9, 25, 25, 95, 201, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 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]) total number of confs: 962 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567900 none O=C1N=C(CCNS(=O)(=O)C2=CC=C(Br)C([N+](=O)[O-])=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 17, 1, 8, 11, 11, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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: [201, 201, 201, 83, 50, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 201, 201, 83, 83, 50, 50, 9, 1, 1, 1] 201 rigid atoms, others: [7, 10, 11, 12, 13, 14, 15, 16, 19, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 17, 18, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 541 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567900 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567900 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567900/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567900 Building REAL300025567901 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567901' /scratch/stefan/7901150/working/building/REAL300025567901 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567901 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567901/0 /scratch/stefan/7901150/working/building/REAL300025567901 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 425) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/425 `/scratch/stefan/7901150/working/3D/425' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2=CC=CC3=CC=C(Cl)C=C32)[N-]O1) `REAL300025567901.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567901.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567901/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567901 none O=C1N=C(CCNS(=O)(=O)C2=CC=CC3=CC=C(Cl)C=C32)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 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 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, 9, 23, 75, 130, 130, 130, 130, 130, 130, 130, 130, 130, 130, 130, 130, 130, 1, 1, 9, 9, 23, 23, 75, 130, 130, 130, 130, 130, 130] 130 rigid atoms, others: [0, 1, 2, 3, 4, 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]) total number of confs: 535 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567901 none O=C1N=C(CCNS(=O)(=O)C2=CC=CC3=CC=C(Cl)C=C32)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 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 130 conformations in input total number of sets (complete confs): 130 using faster count positions algorithm for large data unique positions, atoms: [130, 130, 130, 51, 29, 7, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 130, 130, 51, 51, 29, 29, 7, 1, 1, 1, 1, 1, 1] 130 rigid atoms, others: [32, 33, 7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 351 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567901 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567901 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567901/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567901 Building REAL300025567902 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567902' /scratch/stefan/7901150/working/building/REAL300025567902 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567902 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567902/0 /scratch/stefan/7901150/working/building/REAL300025567902 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 426) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/426 `/scratch/stefan/7901150/working/3D/426' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)C1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1F) `REAL300025567902.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567902.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567902/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567902 none CS(=O)(=O)C1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 15, 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, 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, 1, 7, 7, 1, 1, 1, 1, 1, 2, 2, 2, 9, 45, 67, 176, 176, 176, 176, 176, 1, 1, 1, 7, 7, 7, 1, 1, 9, 45, 45, 67, 67, 1] 201 rigid atoms, others: [1, 33, 4, 5, 6, 7, 8, 20, 21, 22, 26, 27] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 28, 29, 30, 31, 32]) total number of confs: 465 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567902 none CS(=O)(=O)C1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 15, 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, 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, 176, 201, 201, 176, 176, 176, 103, 75, 103, 103, 24, 8, 1, 1, 1, 1, 1, 1, 1, 176, 176, 176, 201, 201, 201, 176, 176, 75, 24, 24, 8, 8, 176] 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: 703 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567902 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567902 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567902/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567902 Building REAL300025567903 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567903' /scratch/stefan/7901150/working/building/REAL300025567903 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567903 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567903/0 /scratch/stefan/7901150/working/building/REAL300025567903 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 427) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/427 `/scratch/stefan/7901150/working/3D/427' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2=CC3=CC(F)=CC=C3S2)[N-]O1) `REAL300025567903.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567903.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567903/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567903 none O=C1N=C(CCNS(=O)(=O)C2=CC3=CC(F)=CC=C3S2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 15, 1, 1, 1, 14, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 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: [1, 1, 1, 1, 1, 9, 24, 72, 123, 123, 123, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 9, 9, 24, 24, 72, 201, 201, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 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]) total number of confs: 618 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567903 none O=C1N=C(CCNS(=O)(=O)C2=CC3=CC(F)=CC=C3S2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 15, 1, 1, 1, 14, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 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: [201, 201, 201, 107, 73, 23, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 107, 107, 73, 73, 23, 1, 1, 1, 1] 201 rigid atoms, others: [7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 646 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567903 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567903 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567903/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567903 Building REAL300025567904 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567904' /scratch/stefan/7901150/working/building/REAL300025567904 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567904 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567904/0 /scratch/stefan/7901150/working/building/REAL300025567904 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 428) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/428 `/scratch/stefan/7901150/working/3D/428' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC(F)=CC=C1S(=O)(=O)NCCC1=NC(=O)O[N-]1) `REAL300025567904.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567904.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567904/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567904 none N#CC1=CC(F)=CC=C1S(=O)(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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: [8, 1, 1, 1, 1, 15, 1, 1, 1, 14, 11, 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, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 5, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 13, 63, 97, 201, 201, 199, 201, 201, 1, 1, 1, 13, 65, 65, 97, 97] 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]) total number of confs: 592 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567904 none N#CC1=CC(F)=CC=C1S(=O)(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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: [8, 1, 1, 1, 1, 15, 1, 1, 1, 14, 11, 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, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 5, 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: [201, 201, 201, 201, 201, 201, 201, 201, 172, 112, 172, 172, 24, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 112, 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]) total number of confs: 691 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567904 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567904 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567904/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567904 Building REAL300025567905 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567905' /scratch/stefan/7901150/working/building/REAL300025567905 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567905 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567905/0 /scratch/stefan/7901150/working/building/REAL300025567905 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 429) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/429 `/scratch/stefan/7901150/working/3D/429' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=NC2=CC(S(=O)(=O)NCCC3=NC(=O)O[N-]3)=CC=C21) `REAL300025567905.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567905.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567905/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567905 none CN1C=NC2=CC(S(=O)(=O)NCCC3=NC(=O)O[N-]3)=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 1, 14, 11, 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, 6, 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, 2, 2, 2, 9, 52, 86, 201, 201, 201, 201, 201, 1, 1, 1, 2, 2, 2, 1, 1, 9, 52, 52, 86, 86, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 32, 33, 19, 20, 21, 25, 26] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 27, 28, 29, 30, 31]) total number of confs: 550 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567905 none CN1C=NC2=CC(S(=O)(=O)NCCC3=NC(=O)O[N-]3)=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 1, 14, 11, 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, 6, 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, 134, 93, 134, 134, 24, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 93, 25, 25, 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]) total number of confs: 653 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567905 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567905 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567905/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567905 Building REAL300025567906 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567906' /scratch/stefan/7901150/working/building/REAL300025567906 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567906 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567906/0 /scratch/stefan/7901150/working/building/REAL300025567906 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 430) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/430 `/scratch/stefan/7901150/working/3D/430' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)C1=CC=C(Cl)C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=C1) `REAL300025567906.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567906.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567906/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567906 none CC(=O)C1=CC=C(Cl)C(S(=O)(=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', 'Cl', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 1, 11, 1, 1, 1, 1, 16, 1, 14, 11, 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, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 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 110 conformations in input total number of sets (complete confs): 110 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 15, 33, 37, 84, 84, 84, 84, 84, 1, 10, 10, 10, 1, 1, 15, 33, 33, 37, 37, 1] 110 rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 9, 21, 25, 26] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 27, 28, 29, 30, 31]) total number of confs: 238 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567906 none CC(=O)C1=CC=C(Cl)C(S(=O)(=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', 'Cl', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 1, 11, 1, 1, 1, 1, 16, 1, 14, 11, 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, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 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 110 conformations in input total number of sets (complete confs): 110 using faster count positions algorithm for large data unique positions, atoms: [110, 84, 110, 84, 84, 84, 84, 84, 70, 53, 70, 70, 22, 8, 1, 1, 1, 1, 1, 1, 1, 84, 110, 110, 110, 84, 84, 53, 22, 22, 8, 8, 84] 110 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: 405 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567906 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567906 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567906/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567906 Building REAL300025567907 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567907' /scratch/stefan/7901150/working/building/REAL300025567907 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567907 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567907/0 /scratch/stefan/7901150/working/building/REAL300025567907 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 431) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/431 `/scratch/stefan/7901150/working/3D/431' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1N=CC2=CC(S(=O)(=O)NCCC3=NC(=O)O[N-]3)=CC=C21) `REAL300025567907.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567907/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567907 none CC(C)N1N=CC2=CC(S(=O)(=O)NCCC3=NC(=O)O[N-]3)=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 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, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 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: [5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 45, 84, 201, 201, 201, 201, 201, 1, 1, 1, 5, 5, 5, 5, 6, 6, 6, 1, 1, 9, 45, 45, 84, 84, 1, 1] 201 rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 9, 39, 21, 22, 23, 38, 31] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37]) total number of confs: 570 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567907 none CC(C)N1N=CC2=CC(S(=O)(=O)NCCC3=NC(=O)O[N-]3)=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 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, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 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, 124, 81, 124, 124, 24, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 81, 24, 24, 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]) total number of confs: 634 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567907 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567907 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567907/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567907 Building REAL300025567908 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567908' /scratch/stefan/7901150/working/building/REAL300025567908 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567908 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567908/0 /scratch/stefan/7901150/working/building/REAL300025567908 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 432) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/432 `/scratch/stefan/7901150/working/3D/432' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(Cl)=C([N+](=O)[O-])C=C1S(=O)(=O)NCCC1=NC(=O)O[N-]1) `REAL300025567908.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567908.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567908/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567908 none CC1=CC(Cl)=C([N+](=O)[O-])C=C1S(=O)(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', '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, 1, 16, 1, 8, 11, 11, 1, 1, 14, 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: [7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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, 2, 2, 1, 1, 1, 5, 5, 5, 11, 47, 77, 165, 165, 165, 165, 165, 2, 2, 2, 1, 1, 11, 49, 49, 77, 77] 165 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 9, 10, 11, 26, 27] set([32, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31]) total number of confs: 480 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567908 none CC1=CC(Cl)=C([N+](=O)[O-])C=C1S(=O)(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', '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, 1, 16, 1, 8, 11, 11, 1, 1, 14, 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: [7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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, 163, 163, 165, 165, 165, 165, 165, 163, 108, 163, 163, 24, 8, 1, 1, 1, 1, 1, 1, 1, 165, 165, 165, 165, 165, 108, 24, 24, 8, 8] 165 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: 605 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567908 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567908 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567908/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567908 Building REAL300025567909 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567909' /scratch/stefan/7901150/working/building/REAL300025567909 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567909 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567909/0 /scratch/stefan/7901150/working/building/REAL300025567909 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 433) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/433 `/scratch/stefan/7901150/working/3D/433' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=C([N+](=O)[O-])C=CC=C1S(=O)(=O)NCCC1=NC(=O)O[N-]1) `REAL300025567909.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567909.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567909/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567909 none N#CC1=C([N+](=O)[O-])C=CC=C1S(=O)(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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: [8, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 14, 11, 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, 3, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 5, 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: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 5, 5, 5, 13, 55, 73, 158, 158, 158, 158, 158, 1, 1, 1, 13, 57, 57, 73, 73] 158 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 11, 23, 24, 25] set([5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30]) total number of confs: 447 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567909 none N#CC1=C([N+](=O)[O-])C=CC=C1S(=O)(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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: [8, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 14, 11, 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, 3, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 5, 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: [158, 158, 158, 158, 158, 158, 158, 158, 158, 158, 138, 82, 138, 138, 24, 8, 1, 1, 1, 1, 1, 1, 1, 158, 158, 158, 82, 24, 24, 8, 8] 158 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]) total number of confs: 591 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567909 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567909 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567909/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567909 Building REAL300025567910 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567910' /scratch/stefan/7901150/working/building/REAL300025567910 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567910 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567910/0 /scratch/stefan/7901150/working/building/REAL300025567910 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 434) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/434 `/scratch/stefan/7901150/working/3D/434' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(Cl)=CC=C1S(=O)(=O)NCCC1=NC(=O)O[N-]1) `REAL300025567910.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567910/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567910 none COC(=O)C1=CC(Cl)=CC=C1S(=O)(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.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, 11, 1, 1, 1, 16, 1, 1, 1, 14, 11, 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, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 11, 39, 63, 140, 140, 140, 140, 140, 7, 7, 7, 1, 1, 1, 11, 41, 41, 63, 63] 201 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 11, 26, 27, 28] set([0, 1, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33]) total number of confs: 428 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567910 none COC(=O)C1=CC(Cl)=CC=C1S(=O)(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.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, 11, 1, 1, 1, 16, 1, 1, 1, 14, 11, 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, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 140, 201, 140, 140, 112, 140, 140, 140, 110, 74, 110, 110, 22, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 140, 140, 140, 74, 22, 22, 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: 884 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567910 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567910 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567910/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567910 Building REAL300025567911 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567911' /scratch/stefan/7901150/working/building/REAL300025567911 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025567911 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567911/0 /scratch/stefan/7901150/working/building/REAL300025567911 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 435) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/435 `/scratch/stefan/7901150/working/3D/435' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2=C(Cl)C=CN=C2Cl)[N-]O1) `REAL300025567911.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567911.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567911/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567911 none O=C1N=C(CCNS(=O)(=O)C2=C(Cl)C=CN=C2Cl)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 16, 1, 1, 8, 1, 16, 8, 12, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 3, 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: [1, 1, 1, 1, 1, 9, 23, 79, 138, 138, 138, 201, 201, 201, 201, 201, 201, 201, 1, 1, 9, 9, 23, 23, 79, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 18, 19] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 641 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567911 none O=C1N=C(CCNS(=O)(=O)C2=C(Cl)C=CN=C2Cl)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 16, 1, 1, 8, 1, 16, 8, 12, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 3, 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: [201, 201, 201, 116, 83, 23, 10, 1, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 116, 116, 83, 83, 23, 1, 1] 201 rigid atoms, others: [7, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 665 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567911 /scratch/stefan/7901150/working /scratch/stefan/7901150 mkdir: created directory `1' /scratch/stefan/7901150/working/building/REAL300025567911/1 /scratch/stefan/7901150/working/building/REAL300025567911 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 1 (index: 436) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/436 `/scratch/stefan/7901150/working/3D/436' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CC[N-]S(=O)(=O)C2=C(Cl)C=CN=C2Cl)[N-]O1) `REAL300025567911.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025567911.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567911/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567911 none O=C1N=C(CC[N-]S(=O)(=O)C2=C(Cl)C=CN=C2Cl)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 16, 1, 1, 8, 1, 16, 8, 12, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 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: [1, 1, 1, 1, 1, 9, 13, 51, 113, 113, 113, 176, 176, 176, 176, 176, 176, 176, 1, 1, 9, 9, 13, 13, 176, 176] 176 rigid atoms, others: [0, 1, 2, 3, 4, 18, 19] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25]) total number of confs: 512 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567911 none O=C1N=C(CC[N-]S(=O)(=O)C2=C(Cl)C=CN=C2Cl)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 16, 1, 1, 8, 1, 16, 8, 12, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 176 conformations in input total number of sets (complete confs): 176 using faster count positions algorithm for large data unique positions, atoms: [176, 176, 176, 87, 85, 25, 10, 1, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 176, 176, 87, 87, 85, 85, 1, 1] 176 rigid atoms, others: [7, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 18, 19, 20, 21, 22, 23]) total number of confs: 474 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567911 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567911 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 1: /scratch/stefan/7901150/working/building/REAL300025567911/1.* 0: /scratch/stefan/7901150/working/building/REAL300025567911/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567911 Building REAL300025567912 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567912' /scratch/stefan/7901150/working/building/REAL300025567912 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567912 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567912/0 /scratch/stefan/7901150/working/building/REAL300025567912 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 437) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/437 `/scratch/stefan/7901150/working/3D/437' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=NC=CC2=C(S(=O)(=O)NCCC3=NC(=O)O[N-]3)C=CC=C21) `REAL300025567912.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567912.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567912/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567912 none COC(=O)C1=NC=CC2=C(S(=O)(=O)NCCC3=NC(=O)O[N-]3)C=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 11, 1, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 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, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 25, 43, 104, 104, 104, 104, 104, 1, 1, 1, 1, 9, 9, 9, 1, 1, 5, 25, 25, 43, 43, 1, 1, 1] 201 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 37, 22, 23, 24, 25, 38, 29, 30, 36] set([0, 1, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 31, 32, 33, 34, 35]) total number of confs: 300 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567912 none COC(=O)C1=NC=CC2=C(S(=O)(=O)NCCC3=NC(=O)O[N-]3)C=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 11, 1, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 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, 104, 201, 104, 104, 104, 104, 104, 104, 56, 104, 104, 21, 8, 1, 1, 1, 1, 1, 1, 1, 104, 104, 104, 104, 201, 201, 201, 104, 104, 56, 22, 21, 8, 8, 104, 104, 104] 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: 758 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567912 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567912 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567912/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567912 Building REAL300025567913 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567913' /scratch/stefan/7901150/working/building/REAL300025567913 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567913 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567913/0 /scratch/stefan/7901150/working/building/REAL300025567913 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 438) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/438 `/scratch/stefan/7901150/working/3D/438' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCS(=O)(=O)NCCC1=NC(=O)O[N-]1)OCC1=CC=CC=C1) `REAL300025567913.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567913.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567913/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567913 none O=C(NCCS(=O)(=O)NCCC1=NC(=O)O[N-]1)OCC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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: [11, 1, 8, 5, 5, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 12, 5, 1, 1, 1, 1, 1, 1, 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, 6, 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, 7, 7] 0 hydrogens 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, 110, 64, 64, 25, 17, 25, 25, 11, 7, 1, 1, 1, 1, 1, 1, 1, 155, 155, 201, 201, 201, 201, 201, 201, 110, 64, 64, 64, 64, 17, 11, 11, 7, 7, 201, 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, 41]) total number of confs: 837 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567913 none O=C(NCCS(=O)(=O)NCCC1=NC(=O)O[N-]1)OCC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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: [11, 1, 8, 5, 5, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 12, 5, 1, 1, 1, 1, 1, 1, 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, 6, 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, 7, 7] 0 hydrogens 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, 13, 42, 42, 75, 75, 75, 116, 123, 123, 201, 201, 201, 201, 201, 3, 1, 1, 1, 1, 1, 1, 1, 13, 42, 42, 42, 42, 116, 123, 123, 123, 123, 3, 3, 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: 674 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567913 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567913 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567913/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567913 Building REAL300025567914 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567914' /scratch/stefan/7901150/working/building/REAL300025567914 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567914 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567914/0 /scratch/stefan/7901150/working/building/REAL300025567914 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 439) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/439 `/scratch/stefan/7901150/working/3D/439' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)CC2=CC=C(Cl)C=C2Br)[N-]O1) `REAL300025567914.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567914.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567914/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567914 none O=C1N=C(CCNS(=O)(=O)CC2=CC=C(Cl)C=C2Br)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Br', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 5, 1, 1, 1, 1, 16, 1, 1, 17, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 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: [1, 1, 1, 1, 1, 8, 21, 75, 109, 109, 109, 141, 201, 201, 201, 201, 201, 201, 201, 1, 1, 8, 8, 21, 21, 75, 141, 141, 201, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 19, 20] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 712 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567914 none O=C1N=C(CCNS(=O)(=O)CC2=CC=C(Cl)C=C2Br)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Br', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 5, 1, 1, 1, 1, 16, 1, 1, 17, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 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: [201, 201, 201, 117, 99, 37, 12, 4, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 117, 117, 99, 99, 37, 4, 4, 1, 1, 1] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 663 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567914 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567914 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567914/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567914 Building REAL300025567915 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567915' /scratch/stefan/7901150/working/building/REAL300025567915 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567915 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567915/0 /scratch/stefan/7901150/working/building/REAL300025567915 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 440) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/440 `/scratch/stefan/7901150/working/3D/440' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1C=NC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=C1) `REAL300025567915.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567915/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567915 none CC(C)N1C=NC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 5, 5, 8, 1, 8, 1, 14, 11, 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, 6, 6, 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, 1, 10, 1, 1, 1, 1, 1, 6, 6, 6, 23, 71, 83, 185, 185, 185, 185, 185, 1, 11, 11, 11, 10, 11, 11, 11, 1, 23, 71, 71, 83, 83, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 19, 33, 27] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32]) total number of confs: 531 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567915 none CC(C)N1C=NC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 5, 5, 8, 1, 8, 1, 14, 11, 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, 6, 6, 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, 185, 201, 185, 185, 185, 131, 79, 131, 131, 22, 8, 1, 1, 1, 1, 1, 1, 1, 185, 201, 201, 201, 201, 201, 201, 201, 185, 79, 23, 23, 8, 8, 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]) total number of confs: 694 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567915 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567915 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567915/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567915 Building REAL300025567916 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567916' /scratch/stefan/7901150/working/building/REAL300025567916 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567916 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567916/0 /scratch/stefan/7901150/working/building/REAL300025567916 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 441) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/441 `/scratch/stefan/7901150/working/3D/441' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2=CC(F)=CC(Cl)=C2)[N-]O1) `REAL300025567916.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567916.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567916/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567916 none O=C1N=C(CCNS(=O)(=O)C2=CC(F)=CC(Cl)=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 15, 1, 1, 16, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 9, 25, 75, 106, 106, 106, 201, 201, 201, 201, 201, 201, 201, 1, 1, 9, 9, 25, 25, 75, 201, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 18, 19] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 621 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567916 none O=C1N=C(CCNS(=O)(=O)C2=CC(F)=CC(Cl)=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 15, 1, 1, 16, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 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: [201, 201, 201, 84, 49, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 84, 84, 49, 49, 9, 1, 1, 1] 201 rigid atoms, others: [7, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 542 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567916 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567916 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567916/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567916 Building REAL300025567917 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567917' /scratch/stefan/7901150/working/building/REAL300025567917 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567917 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567917/0 /scratch/stefan/7901150/working/building/REAL300025567917 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 442) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/442 `/scratch/stefan/7901150/working/3D/442' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C(=O)C2=CC=CC3=C(S(=O)(=O)NCCC4=NC(=O)O[N-]4)C=CC1=C23) `REAL300025567917.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567917.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567917/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567917 none CN1C(=O)C2=CC=CC3=C(S(=O)(=O)NCCC4=NC(=O)O[N-]4)C=CC1=C23 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', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 14, 11, 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] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 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, 1, 1, 1, 1, 1, 5, 5, 5, 15, 63, 101, 201, 201, 201, 201, 201, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 15, 63, 63, 101, 101, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 37, 22, 23, 24, 25, 38, 29, 30, 31] set([32, 33, 34, 35, 36, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28]) total number of confs: 618 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567917 none CN1C(=O)C2=CC=CC3=C(S(=O)(=O)NCCC4=NC(=O)O[N-]4)C=CC1=C23 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', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 14, 11, 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] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 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, 201, 201, 201, 149, 90, 149, 149, 24, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 90, 25, 25, 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]) total number of confs: 693 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567917 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567917 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567917/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567917 Building REAL300025567918 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567918' /scratch/stefan/7901150/working/building/REAL300025567918 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567918 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567918/0 /scratch/stefan/7901150/working/building/REAL300025567918 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 443) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/443 `/scratch/stefan/7901150/working/3D/443' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)C1=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=C(Cl)S1) `REAL300025567918.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567918.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567918/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567918 none CS(=O)(=O)C1=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=C(Cl)S1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 16, 14, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 6, 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 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 3, 3, 3, 1, 5, 5, 5, 5, 5] 5 rigid atoms, others: [1, 4, 5, 6, 7, 19, 20, 21, 25] set([0, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 26, 27, 28, 29, 30]) total number of confs: 27 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567918 none CS(=O)(=O)C1=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=C(Cl)S1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 16, 14, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 6, 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 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5] 5 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: 16 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567918 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567918 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567918/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567918 Building REAL300025567919 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567919' /scratch/stefan/7901150/working/building/REAL300025567919 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025567919 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567919/0 /scratch/stefan/7901150/working/building/REAL300025567919 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 444) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/444 `/scratch/stefan/7901150/working/3D/444' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CC[N-]S(=O)(=O)C2=CC(F)=C(Br)C=C2F)[N-]O1) `REAL300025567919.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567919.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567919/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567919 none O=C1N=C(CC[N-]S(=O)(=O)C2=CC(F)=C(Br)C=C2F)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 15, 1, 17, 1, 1, 15, 8, 12, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 9, 13, 34, 87, 87, 87, 131, 131, 131, 131, 131, 131, 131, 131, 1, 1, 9, 9, 13, 13, 131, 131] 131 rigid atoms, others: [0, 1, 2, 3, 4, 19, 20] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26]) total number of confs: 397 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567919 none O=C1N=C(CC[N-]S(=O)(=O)C2=CC(F)=C(Br)C=C2F)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 15, 1, 17, 1, 1, 15, 8, 12, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 71, 67, 23, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 131, 131, 71, 71, 67, 67, 1, 1] 131 rigid atoms, others: [7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 19, 20, 21, 22, 23, 24]) total number of confs: 360 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567919 /scratch/stefan/7901150/working /scratch/stefan/7901150 mkdir: created directory `1' /scratch/stefan/7901150/working/building/REAL300025567919/1 /scratch/stefan/7901150/working/building/REAL300025567919 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 1 (index: 445) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/445 `/scratch/stefan/7901150/working/3D/445' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2=CC(F)=C(Br)C=C2F)[N-]O1) `REAL300025567919.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025567919.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567919/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567919 none O=C1N=C(CCNS(=O)(=O)C2=CC(F)=C(Br)C=C2F)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 15, 1, 17, 1, 1, 15, 8, 12, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 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: [1, 1, 1, 1, 1, 9, 25, 80, 139, 139, 139, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 9, 9, 25, 25, 80, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 19, 20] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 678 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567919 none O=C1N=C(CCNS(=O)(=O)C2=CC(F)=C(Br)C=C2F)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 15, 1, 17, 1, 1, 15, 8, 12, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 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: [201, 201, 201, 96, 66, 23, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 96, 96, 66, 66, 23, 1, 1] 201 rigid atoms, others: [7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 585 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567919 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567919 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 1: /scratch/stefan/7901150/working/building/REAL300025567919/1.* 0: /scratch/stefan/7901150/working/building/REAL300025567919/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567919 Building REAL300025567920 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567920' /scratch/stefan/7901150/working/building/REAL300025567920 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567920 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567920/0 /scratch/stefan/7901150/working/building/REAL300025567920 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 446) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/446 `/scratch/stefan/7901150/working/3D/446' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1CC) `REAL300025567920.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567920.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567920/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567920 none CCC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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: [5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 5, 5, 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, 6, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 9, 31, 54, 103, 103, 103, 103, 103, 1, 1, 1, 5, 3, 3, 3, 3, 3, 1, 1, 9, 31, 31, 54, 54, 1, 5, 5, 5, 5, 5] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 34, 18, 19, 20, 27, 28] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39]) total number of confs: 358 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567920 none CCC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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: [5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 5, 5, 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, 6, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 103, 102, 103, 103, 57, 37, 57, 57, 12, 6, 1, 1, 1, 1, 1, 1, 1, 103, 103, 103, 201, 197, 197, 197, 197, 197, 103, 103, 37, 12, 12, 6, 6, 103, 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]) total number of confs: 1467 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567920 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567920 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567920/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567920 Building REAL300025567921 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567921' /scratch/stefan/7901150/working/building/REAL300025567921 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567921 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567921/0 /scratch/stefan/7901150/working/building/REAL300025567921 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 447) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/447 `/scratch/stefan/7901150/working/3D/447' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=CC([N+](=O)[O-])=C1F) `REAL300025567921.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567921.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567921/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567921 none CC1=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=CC([N+](=O)[O-])=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 11, 11, 1, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in 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, 9, 53, 87, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 9, 53, 53, 87, 87, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 32, 16, 17, 18, 19, 20, 21, 22, 26] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 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 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567921 none CC1=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=CC([N+](=O)[O-])=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 11, 11, 1, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 132, 89, 132, 132, 24, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 89, 24, 24, 8, 8, 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]) total number of confs: 647 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567921 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567921 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567921/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567921 Building REAL300025567922 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567922' /scratch/stefan/7901150/working/building/REAL300025567922 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567922 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567922/0 /scratch/stefan/7901150/working/building/REAL300025567922 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 448) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/448 `/scratch/stefan/7901150/working/3D/448' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=N1) `REAL300025567922.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567922.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567922/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567922 none COC(=O)C1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.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, 12, 1, 11, 1, 1, 1, 1, 14, 11, 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, 3, 7, 5, 7, 7, 7, 7, 7, 6, 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: [7, 7, 1, 7, 1, 1, 1, 1, 1, 2, 2, 2, 9, 44, 75, 160, 160, 160, 160, 160, 1, 1, 7, 7, 7, 1, 1, 9, 44, 44, 75, 75, 1] 201 rigid atoms, others: [32, 2, 4, 5, 6, 7, 8, 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]) total number of confs: 478 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567922 none COC(=O)C1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.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, 12, 1, 11, 1, 1, 1, 1, 14, 11, 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, 3, 7, 5, 7, 7, 7, 7, 7, 6, 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, 201, 160, 201, 160, 160, 160, 103, 70, 103, 103, 24, 8, 1, 1, 1, 1, 1, 1, 1, 160, 160, 201, 201, 201, 160, 160, 70, 25, 25, 8, 8, 160] 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: 690 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567922 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567922 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567922/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567922 Building REAL300025567923 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567923' /scratch/stefan/7901150/working/building/REAL300025567923 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025567923 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567923/0 /scratch/stefan/7901150/working/building/REAL300025567923 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 449) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/449 `/scratch/stefan/7901150/working/3D/449' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=COC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=C1) `REAL300025567923.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567923.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567923/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567923 none COC(=O)C1=COC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 12, 1, 14, 11, 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, 5, 7, 7, 3, 7, 7, 6, 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: [2, 2, 1, 2, 1, 1, 1, 1, 1, 6, 6, 6, 25, 71, 86, 185, 185, 185, 185, 185, 1, 3, 3, 3, 1, 25, 71, 71, 86, 86, 1] 201 rigid atoms, others: [2, 4, 5, 6, 7, 8, 20, 24, 30] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 25, 26, 27, 28, 29]) total number of confs: 536 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567923 none COC(=O)C1=COC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 12, 1, 14, 11, 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, 5, 7, 7, 3, 7, 7, 6, 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, 185, 201, 185, 185, 185, 96, 62, 96, 96, 21, 8, 1, 1, 1, 1, 1, 1, 1, 185, 201, 201, 201, 185, 62, 22, 22, 8, 8, 185] 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: 591 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567923 /scratch/stefan/7901150/working /scratch/stefan/7901150 mkdir: created directory `1' /scratch/stefan/7901150/working/building/REAL300025567923/1 /scratch/stefan/7901150/working/building/REAL300025567923 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 1 (index: 450) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/450 `/scratch/stefan/7901150/working/3D/450' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=COC(S(=O)(=O)[N-]CCC2=NC(=O)O[N-]2)=C1) `REAL300025567923.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025567923.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567923/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567923 none COC(=O)C1=COC(S(=O)(=O)[N-]CCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', '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'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 12, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 3, 7, 7, 3, 3, 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: [8, 8, 1, 8, 1, 1, 1, 1, 1, 6, 6, 6, 25, 81, 81, 169, 169, 169, 169, 169, 1, 9, 9, 9, 1, 81, 81, 81, 81, 1] 201 rigid atoms, others: [2, 4, 5, 6, 7, 8, 20, 24, 29] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 25, 26, 27, 28]) total number of confs: 435 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567923 none COC(=O)C1=COC(S(=O)(=O)[N-]CCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', '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'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 12, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 3, 7, 7, 3, 3, 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: [201, 201, 169, 201, 169, 169, 169, 86, 33, 86, 86, 8, 8, 1, 1, 1, 1, 1, 1, 1, 169, 201, 201, 201, 169, 9, 9, 8, 8, 169] 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: 557 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567923 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567923 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 1: /scratch/stefan/7901150/working/building/REAL300025567923/1.* 0: /scratch/stefan/7901150/working/building/REAL300025567923/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567923 Building REAL300025567924 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567924' /scratch/stefan/7901150/working/building/REAL300025567924 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567924 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567924/0 /scratch/stefan/7901150/working/building/REAL300025567924 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 451) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/451 `/scratch/stefan/7901150/working/3D/451' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C(F)C(CS(=O)(=O)NCCC2=NC(=O)O[N-]2)=C1) `REAL300025567924.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567924.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567924/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567924 none N#CC1=CC=C(F)C(CS(=O)(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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: [8, 1, 1, 1, 1, 1, 15, 1, 5, 14, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 1, 1, 1, 1, 5, 13, 13, 13, 36, 92, 111, 201, 201, 201, 201, 201, 1, 1, 1, 5, 5, 36, 92, 92, 111, 111, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 21, 22, 23, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 631 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567924 none N#CC1=CC=C(F)C(CS(=O)(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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: [8, 1, 1, 1, 1, 1, 15, 1, 5, 14, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 155, 105, 71, 105, 105, 22, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 155, 155, 71, 23, 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]) total number of confs: 789 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567924 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567924 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567924/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567924 Building REAL300025567925 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567925' /scratch/stefan/7901150/working/building/REAL300025567925 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567925 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567925/0 /scratch/stefan/7901150/working/building/REAL300025567925 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 452) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/452 `/scratch/stefan/7901150/working/3D/452' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=NN(C)C(CC)=C1S(=O)(=O)NCCC1=NC(=O)O[N-]1) `REAL300025567925.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567925/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567925 none CCC1=NN(C)C(CC)=C1S(=O)(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', '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, 1, 8, 8, 5, 1, 5, 5, 1, 14, 11, 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, 6, 6, 4, 7, 7, 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, 3, 1, 1, 8, 8, 8, 12, 42, 57, 158, 158, 158, 158, 158, 5, 5, 5, 5, 5, 2, 2, 2, 3, 3, 3, 3, 3, 12, 42, 42, 57, 57] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 9, 10] set([0, 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, 35, 36, 37, 38, 39]) total number of confs: 431 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567925 none CCC1=NN(C)C(CC)=C1S(=O)(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', '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, 1, 8, 8, 5, 1, 5, 5, 1, 14, 11, 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, 6, 6, 4, 7, 7, 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: [187, 158, 158, 158, 158, 158, 158, 158, 175, 118, 76, 118, 118, 22, 8, 1, 1, 1, 1, 1, 1, 1, 187, 187, 187, 187, 187, 158, 158, 158, 175, 175, 175, 175, 175, 76, 22, 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, 37, 38, 39]) total number of confs: 801 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567925 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567925 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567925/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567925 Building REAL300025567926 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567926' /scratch/stefan/7901150/working/building/REAL300025567926 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567926 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567926/0 /scratch/stefan/7901150/working/building/REAL300025567926 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 453) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/453 `/scratch/stefan/7901150/working/3D/453' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2=CC=C([N+](=O)[O-])C=C2Br)[N-]O1) `REAL300025567926.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567926.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567926/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567926 none O=C1N=C(CCNS(=O)(=O)C2=CC=C([N+](=O)[O-])C=C2Br)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'Br', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 17, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 3, 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: [1, 1, 1, 1, 1, 9, 25, 87, 117, 117, 117, 117, 117, 117, 117, 117, 117, 117, 117, 117, 1, 1, 9, 9, 25, 25, 87, 117, 117, 117] 117 rigid atoms, others: [0, 1, 2, 3, 4, 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]) total number of confs: 446 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567926 none O=C1N=C(CCNS(=O)(=O)C2=CC=C([N+](=O)[O-])C=C2Br)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'Br', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 17, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 117 conformations in input total number of sets (complete confs): 117 using faster count positions algorithm for large data unique positions, atoms: [117, 117, 117, 53, 31, 5, 3, 1, 3, 3, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 117, 117, 53, 53, 31, 31, 5, 1, 1, 1] 117 rigid atoms, others: [7, 10, 11, 12, 13, 14, 17, 18, 19, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 15, 16, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 338 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567926 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567926 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567926/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567926 Building REAL300025567927 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567927' /scratch/stefan/7901150/working/building/REAL300025567927 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567927 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567927/0 /scratch/stefan/7901150/working/building/REAL300025567927 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 454) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/454 `/scratch/stefan/7901150/working/3D/454' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2=CC=C([N+](=O)[O-])C=C2C(F)(F)F)[N-]O1) `REAL300025567927.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567927.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567927/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567927 none O=C1N=C(CCNS(=O)(=O)C2=CC=C([N+](=O)[O-])C=C2C(F)(F)F)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 5, 15, 15, 15, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 3, 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: [1, 1, 1, 1, 1, 9, 23, 77, 105, 105, 105, 105, 105, 105, 105, 105, 105, 105, 105, 105, 105, 105, 105, 1, 1, 9, 9, 23, 23, 77, 105, 105, 105] 105 rigid atoms, others: [0, 1, 2, 3, 4, 23, 24] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 414 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567927 none O=C1N=C(CCNS(=O)(=O)C2=CC=C([N+](=O)[O-])C=C2C(F)(F)F)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 5, 15, 15, 15, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 105 conformations in input total number of sets (complete confs): 105 using faster count positions algorithm for large data unique positions, atoms: [105, 105, 105, 49, 29, 5, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 105, 105, 49, 49, 29, 29, 5, 1, 1, 1] 105 rigid atoms, others: [32, 7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 320 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567927 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567927 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567927/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567927 Building REAL300025567928 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567928' /scratch/stefan/7901150/working/building/REAL300025567928 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567928 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567928/0 /scratch/stefan/7901150/working/building/REAL300025567928 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 455) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/455 `/scratch/stefan/7901150/working/3D/455' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=CN=C1COC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1) `REAL300025567928.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567928/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567928 none CN1N=CN=C1COC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'N.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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: [5, 8, 8, 1, 8, 1, 5, 12, 1, 1, 1, 1, 14, 11, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 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, 1, 6, 6, 7, 7, 6, 6, 9, 9, 9, 25, 63, 93, 201, 201, 201, 201, 201, 7, 7, 2, 2, 2, 1, 6, 6, 7, 7, 25, 63, 63, 93, 93, 7, 7] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 632 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567928 none CN1N=CN=C1COC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'N.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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: [5, 8, 8, 1, 8, 1, 5, 12, 1, 1, 1, 1, 14, 11, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 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, 7, 7, 7, 7, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 27, 45, 147, 147, 147, 147, 147, 1, 1, 7, 7, 7, 7, 2, 2, 1, 1, 9, 27, 27, 45, 45, 1, 1] 201 rigid atoms, others: [32, 33, 7, 8, 9, 10, 11, 12, 40, 24, 25, 39] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38]) 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567928 none CN1N=CN=C1COC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'N.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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: [5, 8, 8, 1, 8, 1, 5, 12, 1, 1, 1, 1, 14, 11, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 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, 147, 147, 89, 89, 147, 147, 89, 60, 89, 89, 20, 8, 1, 1, 1, 1, 1, 1, 1, 147, 147, 201, 201, 201, 201, 147, 147, 147, 147, 60, 20, 20, 8, 8, 147, 147] 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: 880 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567928 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567928 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567928/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567928 Building REAL300025567929 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567929' /scratch/stefan/7901150/working/building/REAL300025567929 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567929 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567929/0 /scratch/stefan/7901150/working/building/REAL300025567929 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 456) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/456 `/scratch/stefan/7901150/working/3D/456' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CC[N-]S(=O)(=O)C2=C(F)C(F)=C(F)C(F)=C2F)[N-]O1) `REAL300025567929.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567929.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567929/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567929 none O=C1N=C(CC[N-]S(=O)(=O)C2=C(F)C(F)=C(F)C(F)=C2F)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'F', 'N.2', 'O.3', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 15, 1, 15, 1, 15, 1, 15, 1, 15, 8, 12, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 1, 9, 13, 37, 95, 95, 95, 127, 127, 127, 127, 96, 104, 127, 127, 127, 127, 1, 1, 9, 9, 13, 13] 127 rigid atoms, others: [0, 1, 2, 3, 4, 21, 22] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26]) total number of confs: 499 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567929 none O=C1N=C(CC[N-]S(=O)(=O)C2=C(F)C(F)=C(F)C(F)=C2F)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'F', 'N.2', 'O.3', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 15, 1, 15, 1, 15, 1, 15, 1, 15, 8, 12, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7] 0 hydrogens need rotated 128 conformations in input total number of sets (complete confs): 128 using faster count positions algorithm for large data unique positions, atoms: [128, 128, 128, 60, 54, 22, 10, 1, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 128, 128, 60, 60, 54, 54] 128 rigid atoms, others: [7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 21, 22, 23, 24, 25, 26]) total number of confs: 330 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567929 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567929 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567929/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567929 Building REAL300025567930 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567930' /scratch/stefan/7901150/working/building/REAL300025567930 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567930 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567930/0 /scratch/stefan/7901150/working/building/REAL300025567930 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 457) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/457 `/scratch/stefan/7901150/working/3D/457' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)C1=CC=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=C1) `REAL300025567930.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567930.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567930/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567930 none CCC(=O)C1=CC=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', '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.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, 5, 1, 11, 1, 1, 1, 1, 1, 14, 11, 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, 3, 7, 7, 7, 7, 7, 7, 6, 6, 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: [14, 6, 1, 6, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 33, 50, 129, 129, 129, 129, 129, 1, 15, 15, 15, 14, 14, 1, 1, 1, 9, 33, 33, 50, 50, 1] 201 rigid atoms, others: [2, 35, 4, 5, 6, 7, 8, 9, 21, 27, 28, 29] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34]) total number of confs: 398 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567930 none CCC(=O)C1=CC=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', '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.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, 5, 1, 11, 1, 1, 1, 1, 1, 14, 11, 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, 3, 7, 7, 7, 7, 7, 7, 6, 6, 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, 192, 129, 192, 129, 129, 129, 129, 79, 55, 79, 79, 18, 8, 1, 1, 1, 1, 1, 1, 1, 129, 201, 201, 201, 201, 201, 129, 129, 129, 55, 18, 18, 8, 8, 129] 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: 720 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567930 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567930 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567930/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567930 Building REAL300025567931 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567931' /scratch/stefan/7901150/working/building/REAL300025567931 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567931 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567931/0 /scratch/stefan/7901150/working/building/REAL300025567931 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 458) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/458 `/scratch/stefan/7901150/working/3D/458' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN1C=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=N1) `REAL300025567931.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567931.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567931/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567931 none COCCN1C=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 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, 6, 6, 4, 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: [20, 10, 8, 1, 1, 1, 1, 1, 2, 2, 2, 9, 33, 45, 131, 131, 131, 131, 131, 1, 1, 20, 20, 20, 10, 10, 8, 8, 1, 9, 33, 33, 45, 45, 1] 201 rigid atoms, others: [34, 3, 4, 5, 6, 7, 19, 20, 28] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33]) total number of confs: 373 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567931 none COCCN1C=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 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, 6, 6, 4, 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, 197, 131, 131, 131, 98, 72, 98, 98, 20, 8, 1, 1, 1, 1, 1, 1, 1, 131, 131, 201, 201, 201, 201, 201, 197, 197, 131, 72, 20, 20, 8, 8, 131] 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]) total number of confs: 792 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567931 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567931 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567931/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567931 Building REAL300025567932 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567932' /scratch/stefan/7901150/working/building/REAL300025567932 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025567932 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567932/0 /scratch/stefan/7901150/working/building/REAL300025567932 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 459) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/459 `/scratch/stefan/7901150/working/3D/459' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C([N+](=O)[O-])=N1) `REAL300025567932.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567932/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567932 none CCN1C=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C([N+](=O)[O-])=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.pl3', 'O.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 11, 11, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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 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, 3, 3, 3, 5, 29, 43, 125, 125, 125, 125, 125, 1, 1, 2, 2, 1, 7, 7, 7, 7, 7, 1, 5, 29, 29, 43, 43] 201 rigid atoms, others: [1, 2, 3, 4, 5, 17, 18, 21, 27] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32]) total number of confs: 327 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567932 none CCN1C=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C([N+](=O)[O-])=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.pl3', 'O.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 11, 11, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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 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, 87, 125, 125, 20, 8, 1, 1, 1, 1, 1, 1, 1, 125, 125, 125, 125, 125, 201, 201, 201, 201, 201, 125, 87, 20, 20, 8, 8] 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: 919 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567932 /scratch/stefan/7901150/working /scratch/stefan/7901150 mkdir: created directory `1' /scratch/stefan/7901150/working/building/REAL300025567932/1 /scratch/stefan/7901150/working/building/REAL300025567932 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 1 (index: 460) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/460 `/scratch/stefan/7901150/working/3D/460' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C=C(S(=O)(=O)[N-]CCC2=NC(=O)O[N-]2)C([N+](=O)[O-])=N1) `REAL300025567932.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025567932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567932/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567932 none CCN1C=C(S(=O)(=O)[N-]CCC2=NC(=O)O[N-]2)C([N+](=O)[O-])=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.pl3', 'O.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 11, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 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 130 conformations in input total number of sets (complete confs): 130 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 1, 1, 1, 1, 5, 5, 5, 7, 25, 25, 95, 95, 95, 95, 95, 1, 1, 2, 2, 1, 9, 9, 9, 9, 9, 1, 25, 25, 25, 25] 130 rigid atoms, others: [1, 2, 3, 4, 5, 17, 18, 21, 27] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 22, 23, 24, 25, 26, 28, 29, 30, 31]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567932 none CCN1C=C(S(=O)(=O)[N-]CCC2=NC(=O)O[N-]2)C([N+](=O)[O-])=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.pl3', 'O.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 11, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 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 130 conformations in input total number of sets (complete confs): 130 using faster count positions algorithm for large data unique positions, atoms: [130, 95, 95, 95, 93, 39, 93, 93, 8, 8, 1, 1, 1, 1, 1, 1, 1, 95, 95, 95, 95, 95, 130, 130, 130, 130, 130, 95, 8, 8, 8, 8] 130 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: 518 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567932 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567932 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 1: /scratch/stefan/7901150/working/building/REAL300025567932/1.* 0: /scratch/stefan/7901150/working/building/REAL300025567932/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567932 Building REAL300025567933 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567933' /scratch/stefan/7901150/working/building/REAL300025567933 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567933 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567933/0 /scratch/stefan/7901150/working/building/REAL300025567933 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 461) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/461 `/scratch/stefan/7901150/working/3D/461' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2=CC(F)=CC=C2Br)[N-]O1) `REAL300025567933.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567933.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567933/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567933 none O=C1N=C(CCNS(=O)(=O)C2=CC(F)=CC=C2Br)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 15, 1, 1, 1, 17, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 9, 23, 93, 129, 129, 129, 132, 132, 132, 132, 132, 132, 132, 1, 1, 9, 9, 23, 23, 93, 132, 132, 132] 132 rigid atoms, others: [0, 1, 2, 3, 4, 18, 19] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 494 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567933 none O=C1N=C(CCNS(=O)(=O)C2=CC(F)=CC=C2Br)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 15, 1, 1, 1, 17, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 58, 35, 7, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 132, 132, 58, 58, 35, 35, 7, 1, 1, 1] 132 rigid atoms, others: [7, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 364 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567933 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567933 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567933/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567933 Building REAL300025567934 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567934' /scratch/stefan/7901150/working/building/REAL300025567934 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567934 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567934/0 /scratch/stefan/7901150/working/building/REAL300025567934 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 462) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/462 `/scratch/stefan/7901150/working/3D/462' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=C1Br) `REAL300025567934.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567934.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567934/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567934 none CC1=CC=CC(S(=O)(=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', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 17, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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 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, 1, 1, 5, 5, 5, 7, 35, 57, 131, 131, 131, 131, 131, 1, 1, 2, 2, 2, 1, 1, 1, 7, 35, 35, 57, 57] 131 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 18, 19, 23, 24, 25] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 26, 27, 28, 29, 30]) total number of confs: 360 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567934 none CC1=CC=CC(S(=O)(=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', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 17, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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 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, 131, 131, 128, 93, 128, 128, 20, 8, 1, 1, 1, 1, 1, 1, 1, 131, 131, 131, 131, 131, 131, 131, 131, 93, 20, 20, 8, 8] 131 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]) total number of confs: 480 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567934 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567934 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567934/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567934 Building REAL300025567935 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567935' /scratch/stefan/7901150/working/building/REAL300025567935 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025567935 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567935/0 /scratch/stefan/7901150/working/building/REAL300025567935 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 463) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/463 `/scratch/stefan/7901150/working/3D/463' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCCN1C=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C(=O)NC1=O) `REAL300025567935.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567935.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567935/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567935 none CCCCCCN1C=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 8, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 13, 9, 4, 2, 1, 1, 1, 1, 1, 4, 4, 4, 15, 47, 51, 105, 105, 105, 105, 105, 1, 1, 1, 1, 1, 11, 13, 13, 13, 13, 13, 13, 8, 8, 4, 4, 2, 2, 1, 15, 47, 47, 51, 51, 1] 201 rigid atoms, others: [5, 6, 39, 8, 9, 7, 45, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44]) total number of confs: 355 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567935 none CCCCCCN1C=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 8, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 6, 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: [200, 201, 188, 175, 163, 105, 105, 105, 80, 54, 80, 80, 17, 8, 1, 1, 1, 1, 1, 1, 1, 105, 105, 105, 105, 105, 200, 201, 201, 201, 201, 201, 201, 188, 188, 175, 175, 163, 163, 105, 54, 17, 18, 8, 8, 105] 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]) total number of confs: 914 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567935 /scratch/stefan/7901150/working /scratch/stefan/7901150 mkdir: created directory `1' /scratch/stefan/7901150/working/building/REAL300025567935/1 /scratch/stefan/7901150/working/building/REAL300025567935 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 1 (index: 464) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/464 `/scratch/stefan/7901150/working/3D/464' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCCN1C=C(S(=O)(=O)[N-]CCC2=NC(=O)O[N-]2)C(=O)NC1=O) `REAL300025567935.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025567935.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567935/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567935 none CCCCCCN1C=C(S(=O)(=O)[N-]CCC2=NC(=O)O[N-]2)C(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 8, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 6, 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: [17, 15, 11, 6, 2, 1, 1, 1, 1, 1, 6, 6, 6, 11, 32, 32, 74, 74, 74, 74, 74, 1, 1, 1, 1, 1, 17, 19, 19, 19, 19, 15, 15, 10, 10, 6, 6, 2, 2, 1, 32, 32, 32, 32, 1] 201 rigid atoms, others: [5, 6, 39, 8, 9, 7, 44, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43]) total number of confs: 267 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567935 none CCCCCCN1C=C(S(=O)(=O)[N-]CCC2=NC(=O)O[N-]2)C(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 8, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 6, 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: [181, 201, 166, 130, 108, 74, 74, 74, 52, 25, 52, 52, 8, 8, 1, 1, 1, 1, 1, 1, 1, 74, 74, 74, 74, 74, 181, 201, 201, 201, 201, 201, 201, 166, 166, 130, 130, 108, 108, 74, 8, 8, 8, 8, 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: 972 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567935 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567935 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 1: /scratch/stefan/7901150/working/building/REAL300025567935/1.* 0: /scratch/stefan/7901150/working/building/REAL300025567935/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567935 Building REAL300025567936 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567936' /scratch/stefan/7901150/working/building/REAL300025567936 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567936 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567936/0 /scratch/stefan/7901150/working/building/REAL300025567936 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 465) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/465 `/scratch/stefan/7901150/working/3D/465' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2=CN(C3CCOCC3)N=C2)[N-]O1) `REAL300025567936.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567936.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567936/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567936 none O=C1N=C(CCNS(=O)(=O)C2=CN(C3CCOCC3)N=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.2', 'C.2', 'N.2', '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, 1, 5, 5, 8, 14, 11, 11, 1, 1, 8, 5, 5, 5, 12, 5, 5, 8, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 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] 0 hydrogens need rotated 201 conformations in 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, 19, 44, 82, 82, 82, 108, 108, 108, 201, 201, 201, 201, 201, 108, 108, 1, 1, 9, 9, 19, 19, 44, 108, 201, 201, 201, 201, 201, 201, 201, 201, 201, 108] 201 rigid atoms, others: [0, 1, 2, 3, 4, 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, 35, 36, 37, 38]) total number of confs: 679 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567936 none O=C1N=C(CCNS(=O)(=O)C2=CN(C3CCOCC3)N=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.2', 'C.2', 'N.2', '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, 1, 5, 5, 8, 14, 11, 11, 1, 1, 8, 5, 5, 5, 12, 5, 5, 8, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [108, 108, 108, 52, 37, 9, 2, 1, 2, 2, 1, 1, 1, 1, 9, 9, 9, 9, 9, 1, 1, 108, 108, 52, 52, 37, 37, 9, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1] 201 rigid atoms, others: [38, 7, 10, 11, 12, 13, 19, 20, 28] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 338 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567936 none O=C1N=C(CCNS(=O)(=O)C2=CN(C3CCOCC3)N=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.2', 'C.2', 'N.2', '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, 1, 5, 5, 8, 14, 11, 11, 1, 1, 8, 5, 5, 5, 12, 5, 5, 8, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 113, 95, 43, 15, 9, 15, 15, 9, 9, 1, 1, 1, 1, 1, 1, 1, 9, 9, 201, 201, 113, 113, 95, 95, 43, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38]) total number of confs: 632 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567936 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567936 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567936/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567936 Building REAL300025567937 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567937' /scratch/stefan/7901150/working/building/REAL300025567937 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567937 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567937/0 /scratch/stefan/7901150/working/building/REAL300025567937 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 466) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/466 `/scratch/stefan/7901150/working/3D/466' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC1=CC=CC=C1)S(=O)(=O)NCCC1=NC(=O)O[N-]1) `REAL300025567937.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567937.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567937/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567937 none CCN(CC1=CC=CC=C1)S(=O)(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', '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, 8, 5, 1, 1, 1, 1, 1, 1, 14, 11, 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, 6, 6, 4, 7, 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 109 conformations in input total number of sets (complete confs): 109 using faster count positions algorithm for large data unique positions, atoms: [25, 13, 3, 1, 1, 1, 1, 1, 1, 1, 13, 37, 37, 37, 53, 53, 53, 90, 90, 90, 90, 90, 25, 25, 25, 25, 25, 3, 3, 1, 1, 1, 1, 1, 53, 53, 53, 53, 53] 109 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]) total number of confs: 336 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567937 none CCN(CC1=CC=CC=C1)S(=O)(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', '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, 8, 5, 1, 1, 1, 1, 1, 1, 14, 11, 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, 6, 6, 4, 7, 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 109 conformations in input total number of sets (complete confs): 109 using faster count positions algorithm for large data unique positions, atoms: [47, 17, 5, 17, 70, 90, 90, 80, 90, 90, 5, 5, 5, 5, 3, 1, 1, 1, 1, 1, 1, 1, 47, 47, 47, 47, 47, 70, 70, 90, 90, 90, 90, 90, 5, 5, 5, 3, 3] 109 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: 489 number of broken/clashed sets: 12 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567937 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567937 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567937/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567937 Building REAL300025567938 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567938' /scratch/stefan/7901150/working/building/REAL300025567938 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567938 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567938/0 /scratch/stefan/7901150/working/building/REAL300025567938 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 467) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/467 `/scratch/stefan/7901150/working/3D/467' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)N2CCC3(CCCCC3)CC2)[N-]O1) `REAL300025567938.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567938.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567938/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567938 none O=C1N=C(CCNS(=O)(=O)N2CCC3(CCCCC3)CC2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 12, 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: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in 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, 23, 83, 143, 143, 143, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 9, 9, 23, 23, 83, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 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, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 663 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567938 none O=C1N=C(CCNS(=O)(=O)N2CCC3(CCCCC3)CC2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 12, 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: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 73, 21, 6, 1, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 105, 105, 73, 73, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [7, 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] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 619 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567938 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567938 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567938/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567938 Building REAL300025567939 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567939' /scratch/stefan/7901150/working/building/REAL300025567939 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025567939 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567939/0 /scratch/stefan/7901150/working/building/REAL300025567939 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 468) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/468 `/scratch/stefan/7901150/working/3D/468' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2=C(F)C=CC=C2Br)[N-]O1) `REAL300025567939.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567939.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567939/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567939 none O=C1N=C(CCNS(=O)(=O)C2=C(F)C=CC=C2Br)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 15, 1, 1, 1, 1, 17, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 9, 25, 102, 179, 179, 179, 201, 201, 201, 179, 201, 201, 201, 1, 1, 9, 9, 25, 25, 102, 201, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 18, 19] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 832 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567939 none O=C1N=C(CCNS(=O)(=O)C2=C(F)C=CC=C2Br)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 15, 1, 1, 1, 1, 17, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 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: [201, 201, 201, 92, 56, 11, 6, 1, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 92, 92, 56, 56, 11, 1, 1, 1] 201 rigid atoms, others: [7, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 581 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567939 /scratch/stefan/7901150/working /scratch/stefan/7901150 mkdir: created directory `1' /scratch/stefan/7901150/working/building/REAL300025567939/1 /scratch/stefan/7901150/working/building/REAL300025567939 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 1 (index: 469) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/469 `/scratch/stefan/7901150/working/3D/469' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CC[N-]S(=O)(=O)C2=C(F)C=CC=C2Br)[N-]O1) `REAL300025567939.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025567939.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567939/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567939 none O=C1N=C(CC[N-]S(=O)(=O)C2=C(F)C=CC=C2Br)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 15, 1, 1, 1, 1, 17, 8, 12, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 104 conformations in input total number of sets (complete confs): 104 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 9, 11, 37, 75, 75, 75, 104, 104, 104, 75, 104, 104, 104, 1, 1, 9, 9, 11, 11, 104, 104, 104] 104 rigid atoms, others: [0, 1, 2, 3, 4, 18, 19] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 448 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567939 none O=C1N=C(CC[N-]S(=O)(=O)C2=C(F)C=CC=C2Br)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 15, 1, 1, 1, 1, 17, 8, 12, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 104 conformations in input total number of sets (complete confs): 104 using faster count positions algorithm for large data unique positions, atoms: [104, 104, 104, 49, 49, 15, 8, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 104, 104, 49, 49, 49, 49, 1, 1, 1] 104 rigid atoms, others: [7, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 18, 19, 20, 21, 22, 23]) total number of confs: 267 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567939 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567939 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 1: /scratch/stefan/7901150/working/building/REAL300025567939/1.* 0: /scratch/stefan/7901150/working/building/REAL300025567939/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567939 Building REAL300025567940 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567940' /scratch/stefan/7901150/working/building/REAL300025567940 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567940 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567940/0 /scratch/stefan/7901150/working/building/REAL300025567940 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 470) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/470 `/scratch/stefan/7901150/working/3D/470' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)CC2=CC(Cl)=CC=C2F)[N-]O1) `REAL300025567940.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567940.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567940/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567940 none O=C1N=C(CCNS(=O)(=O)CC2=CC(Cl)=CC=C2F)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 5, 1, 1, 1, 16, 1, 1, 1, 15, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 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: [1, 1, 1, 1, 1, 8, 22, 73, 109, 109, 109, 133, 201, 201, 201, 201, 201, 201, 201, 1, 1, 8, 8, 22, 22, 73, 133, 133, 201, 192, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 19, 20] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567940 none O=C1N=C(CCNS(=O)(=O)CC2=CC(Cl)=CC=C2F)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 5, 1, 1, 1, 16, 1, 1, 1, 15, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 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: [201, 201, 201, 117, 93, 35, 10, 4, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 117, 117, 93, 93, 35, 4, 4, 1, 1, 1] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 661 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567940 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567940 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567940/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567940 Building REAL300025567941 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567941' /scratch/stefan/7901150/working/building/REAL300025567941 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567941 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567941/0 /scratch/stefan/7901150/working/building/REAL300025567941 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 471) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/471 `/scratch/stefan/7901150/working/3D/471' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2=CC3=NC=C(Cl)N=C3C=C2)[N-]O1) `REAL300025567941.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567941.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567941/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567941 none O=C1N=C(CCNS(=O)(=O)C2=CC3=NC=C(Cl)N=C3C=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 8, 1, 1, 16, 8, 1, 1, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 3, 7, 7, 7, 3, 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: [1, 1, 1, 1, 1, 9, 25, 89, 122, 122, 122, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 9, 9, 25, 25, 89, 201, 201, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 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]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567941 none O=C1N=C(CCNS(=O)(=O)C2=CC3=NC=C(Cl)N=C3C=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 8, 1, 1, 16, 8, 1, 1, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 3, 7, 7, 7, 3, 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: [201, 201, 201, 93, 55, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 93, 93, 55, 55, 9, 1, 1, 1, 1] 201 rigid atoms, others: [7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 569 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567941 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567941 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567941/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567941 Building REAL300025567942 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567942' /scratch/stefan/7901150/working/building/REAL300025567942 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567942 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567942/0 /scratch/stefan/7901150/working/building/REAL300025567942 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 472) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/472 `/scratch/stefan/7901150/working/3D/472' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2=CC=C3N=C(Cl)SC3=C2)[N-]O1) `REAL300025567942.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567942.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567942/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567942 none O=C1N=C(CCNS(=O)(=O)C2=CC=C3N=C(Cl)SC3=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 16, 14, 1, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 9, 25, 84, 125, 125, 125, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 9, 9, 25, 25, 84, 201, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 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]) total number of confs: 640 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567942 none O=C1N=C(CCNS(=O)(=O)C2=CC=C3N=C(Cl)SC3=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 16, 14, 1, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 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: [201, 201, 201, 95, 55, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 95, 95, 55, 55, 9, 1, 1, 1] 201 rigid atoms, others: [7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 578 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567942 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567942 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567942/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567942 Building REAL300025567943 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567943' /scratch/stefan/7901150/working/building/REAL300025567943 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567943 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567943/0 /scratch/stefan/7901150/working/building/REAL300025567943 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 473) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/473 `/scratch/stefan/7901150/working/3D/473' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1Br) `REAL300025567943.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567943.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567943/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567943 none CCOC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1Br NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 5, 12, 1, 1, 1, 1, 14, 11, 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, 3, 7, 7, 7, 7, 7, 6, 6, 4, 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, 7, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 35, 55, 140, 140, 140, 140, 140, 1, 1, 1, 16, 16, 16, 15, 15, 1, 1, 9, 35, 35, 55, 55, 1] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 34, 19, 20, 21, 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]) total number of confs: 420 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567943 none CCOC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1Br NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 5, 12, 1, 1, 1, 1, 14, 11, 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, 3, 7, 7, 7, 7, 7, 6, 6, 4, 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, 199, 140, 140, 140, 140, 89, 62, 89, 89, 20, 8, 1, 1, 1, 1, 1, 1, 1, 140, 140, 140, 201, 201, 201, 201, 201, 140, 140, 62, 20, 20, 8, 8, 140] 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]) total number of confs: 588 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567943 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567943 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567943/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567943 Building REAL300025567944 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567944' /scratch/stefan/7901150/working/building/REAL300025567944 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567944 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567944/0 /scratch/stefan/7901150/working/building/REAL300025567944 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 474) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/474 `/scratch/stefan/7901150/working/3D/474' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C(Cl)=NC=C1S(=O)(=O)NCCC1=NC(=O)O[N-]1) `REAL300025567944.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567944.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567944/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567944 none CN1C(Cl)=NC=C1S(=O)(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'Cl', 'N.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.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, 1, 16, 8, 1, 1, 14, 11, 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, 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, 6, 6, 6, 21, 74, 94, 201, 201, 201, 201, 201, 2, 2, 2, 1, 21, 74, 74, 94, 94] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 22] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27]) total number of confs: 579 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567944 none CN1C(Cl)=NC=C1S(=O)(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'Cl', 'N.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.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, 1, 16, 8, 1, 1, 14, 11, 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, 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, 199, 153, 90, 153, 153, 24, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 90, 24, 24, 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]) total number of confs: 677 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567944 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567944 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567944/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567944 Building REAL300025567945 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567945' /scratch/stefan/7901150/working/building/REAL300025567945 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567945 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567945/0 /scratch/stefan/7901150/working/building/REAL300025567945 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 475) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/475 `/scratch/stefan/7901150/working/3D/475' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)N=C1Cl) `REAL300025567945.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567945.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567945/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567945 none CN1C=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)N=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'C.2', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 1, 16, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 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, 6, 6, 6, 23, 72, 103, 201, 201, 201, 201, 201, 1, 1, 1, 2, 2, 2, 1, 23, 72, 72, 103, 103] 201 rigid atoms, others: [0, 1, 2, 3, 4, 16, 17, 18, 22] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 23, 24, 25, 26, 27]) total number of confs: 604 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567945 none CN1C=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)N=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'C.2', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 1, 16, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 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, 174, 98, 174, 174, 24, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 98, 25, 25, 8, 8] 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]) total number of confs: 728 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567945 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567945 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567945/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567945 Building REAL300025567946 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567946' /scratch/stefan/7901150/working/building/REAL300025567946 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567946 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567946/0 /scratch/stefan/7901150/working/building/REAL300025567946 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 476) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/476 `/scratch/stefan/7901150/working/3D/476' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=C1C#N) `REAL300025567946.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567946.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567946/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567946 none CC1=CC=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=C1C#N NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.1', 'N.1', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 4, 4, 13, 65, 93, 201, 201, 199, 201, 201, 1, 1, 1, 2, 2, 2, 1, 1, 1, 13, 67, 67, 93, 93] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 18, 19, 20, 24, 25, 26] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 27, 28, 29, 30, 31]) total number of confs: 577 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567946 none CC1=CC=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=C1C#N NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.1', 'N.1', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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, 172, 108, 172, 172, 24, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 108, 25, 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, 30, 31]) total number of confs: 702 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567946 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567946 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567946/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567946 Building REAL300025567947 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567947' /scratch/stefan/7901150/working/building/REAL300025567947 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567947 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567947/0 /scratch/stefan/7901150/working/building/REAL300025567947 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 477) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/477 `/scratch/stefan/7901150/working/3D/477' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2=CC=C(C(F)(F)F)C=C2Cl)[N-]O1) `REAL300025567947.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567947.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567947/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567947 none O=C1N=C(CCNS(=O)(=O)C2=CC=C(C(F)(F)F)C=C2Cl)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Cl', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 16, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 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 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, 9, 25, 96, 148, 148, 148, 158, 158, 158, 158, 158, 158, 158, 158, 158, 158, 1, 1, 9, 9, 25, 25, 96, 158, 158, 158] 158 rigid atoms, others: [0, 1, 2, 3, 4, 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]) total number of confs: 576 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567947 none O=C1N=C(CCNS(=O)(=O)C2=CC=C(C(F)(F)F)C=C2Cl)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Cl', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 16, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 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 158 conformations in input total number of sets (complete confs): 158 using faster count positions algorithm for large data unique positions, atoms: [158, 158, 158, 73, 47, 11, 5, 1, 5, 5, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 158, 158, 73, 73, 47, 47, 11, 1, 1, 1] 158 rigid atoms, others: [7, 10, 11, 12, 13, 14, 18, 19, 20, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 462 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567947 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567947 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567947/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567947 Building REAL300025567948 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567948' /scratch/stefan/7901150/working/building/REAL300025567948 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567948 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567948/0 /scratch/stefan/7901150/working/building/REAL300025567948 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 478) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/478 `/scratch/stefan/7901150/working/3D/478' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)C2=CC=C(Br)C(Cl)=C2)[N-]O1) `REAL300025567948.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567948/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567948 none O=C1N=C(CCNS(=O)(=O)C2=CC=C(Br)C(Cl)=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'Cl', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 17, 1, 16, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 9, 25, 82, 116, 116, 116, 201, 201, 201, 201, 201, 201, 201, 1, 1, 9, 9, 25, 25, 82, 201, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 18, 19] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 630 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567948 none O=C1N=C(CCNS(=O)(=O)C2=CC=C(Br)C(Cl)=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'Cl', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 17, 1, 16, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 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: [201, 201, 201, 91, 51, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 91, 91, 51, 51, 9, 1, 1, 1] 201 rigid atoms, others: [7, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 566 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567948 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567948 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567948/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567948 Building REAL300025567949 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567949' /scratch/stefan/7901150/working/building/REAL300025567949 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567949 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567949/0 /scratch/stefan/7901150/working/building/REAL300025567949 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 479) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/479 `/scratch/stefan/7901150/working/3D/479' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)NCC1=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=CC=C1OC) `REAL300025567949.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567949.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567949/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567949 none CCC(=O)NCC1=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=CC=C1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [35, 14, 14, 14, 5, 1, 1, 1, 1, 1, 3, 3, 3, 5, 19, 21, 66, 66, 66, 66, 66, 1, 1, 1, 1, 3, 35, 35, 35, 35, 35, 14, 5, 5, 1, 5, 19, 19, 21, 21, 1, 1, 4, 4, 4] 201 rigid atoms, others: [34, 5, 6, 7, 8, 9, 41, 40, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 42, 43, 44]) total number of confs: 291 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567949 none CCC(=O)NCC1=CC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=CC=C1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 133, 133, 133, 121, 66, 66, 66, 62, 40, 62, 62, 13, 7, 1, 1, 1, 1, 1, 1, 1, 66, 66, 62, 62, 91, 201, 201, 201, 201, 201, 133, 121, 121, 66, 40, 14, 14, 7, 7, 66, 66, 91, 91, 91] 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: 1040 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567949 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567949 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567949/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567949 Building REAL300025567950 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567950' /scratch/stefan/7901150/working/building/REAL300025567950 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567950 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567950/0 /scratch/stefan/7901150/working/building/REAL300025567950 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 480) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/480 `/scratch/stefan/7901150/working/3D/480' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C1CC2=CC(S(=O)(=O)NCCC3=NC(=O)O[N-]3)=CC=C2O1) `REAL300025567950.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567950.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567950/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567950 none CCOC(=O)C1CC2=CC(S(=O)(=O)NCCC3=NC(=O)O[N-]3)=CC=C2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 12, 1, 11, 5, 5, 1, 1, 1, 14, 11, 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, 3, 7, 5, 7, 7, 7, 7, 7, 7, 6, 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: [33, 17, 13, 1, 13, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 21, 22, 55, 55, 55, 55, 55, 1, 1, 1, 1, 33, 33, 33, 33, 33, 1, 1, 1, 1, 9, 21, 21, 22, 22, 1, 1] 201 rigid atoms, others: [32, 33, 34, 3, 5, 6, 7, 8, 9, 10, 40, 41, 22, 23, 24, 25, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39]) total number of confs: 251 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567950 none CCOC(=O)C1CC2=CC(S(=O)(=O)NCCC3=NC(=O)O[N-]3)=CC=C2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 12, 1, 11, 5, 5, 1, 1, 1, 14, 11, 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, 3, 7, 5, 7, 7, 7, 7, 7, 7, 6, 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, 197, 197, 55, 197, 55, 55, 55, 55, 43, 34, 43, 43, 15, 7, 1, 1, 1, 1, 1, 1, 1, 55, 55, 55, 55, 201, 201, 201, 201, 201, 55, 55, 55, 55, 34, 15, 15, 7, 7, 55, 55] 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: 590 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567950 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567950 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567950/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567950 Building REAL300025567951 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567951' /scratch/stefan/7901150/working/building/REAL300025567951 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567951 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567951/0 /scratch/stefan/7901150/working/building/REAL300025567951 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 481) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/481 `/scratch/stefan/7901150/working/3D/481' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)S1) `REAL300025567951.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567951.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567951/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567951 none CC(C)(C)C1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 5, 5, 5, 1, 1, 1, 1, 14, 11, 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, 7, 7, 7, 7, 7, 6, 6, 4, 7, 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, 3, 3, 1, 1, 1, 1, 1, 6, 6, 6, 19, 52, 63, 120, 120, 120, 120, 120, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 19, 52, 52, 63, 63] 201 rigid atoms, others: [1, 4, 5, 6, 7, 8, 20, 30, 31] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36]) total number of confs: 381 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567951 none CC(C)(C)C1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 5, 5, 5, 1, 1, 1, 1, 14, 11, 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, 7, 7, 7, 7, 7, 6, 6, 4, 7, 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, 120, 201, 201, 120, 120, 120, 71, 37, 71, 71, 10, 4, 1, 1, 1, 1, 1, 1, 1, 120, 201, 201, 201, 201, 201, 201, 201, 201, 201, 120, 120, 37, 10, 10, 4, 4] 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: 858 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567951 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567951 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567951/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567951 Building REAL300025567952 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567952' /scratch/stefan/7901150/working/building/REAL300025567952 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567952 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567952/0 /scratch/stefan/7901150/working/building/REAL300025567952 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 482) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/482 `/scratch/stefan/7901150/working/3D/482' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CCNS(=O)(=O)CC2=C(F)C=CC=C2F)[N-]O1) `REAL300025567952.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567952.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567952/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567952 none O=C1N=C(CCNS(=O)(=O)CC2=C(F)C=CC=C2F)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 5, 1, 1, 15, 1, 1, 1, 1, 15, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 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: [1, 1, 1, 1, 1, 9, 25, 104, 163, 163, 163, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 9, 9, 25, 25, 104, 201, 201, 201, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 19, 20] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 832 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567952 none O=C1N=C(CCNS(=O)(=O)CC2=C(F)C=CC=C2F)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 5, 8, 14, 11, 11, 5, 1, 1, 15, 1, 1, 1, 1, 15, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 4, 7, 6, 6, 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: [201, 201, 201, 127, 87, 25, 12, 4, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 127, 127, 87, 87, 25, 4, 4, 1, 1, 1] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 681 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567952 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567952 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567952/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567952 Building REAL300025567953 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567953' /scratch/stefan/7901150/working/building/REAL300025567953 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567953 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567953/0 /scratch/stefan/7901150/working/building/REAL300025567953 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 483) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/483 `/scratch/stefan/7901150/working/3D/483' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN1C=NC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=C1) `REAL300025567953.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567953.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567953/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567953 none CCCN1C=NC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 5, 5, 8, 1, 8, 1, 14, 11, 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, 6, 6, 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, 7, 1, 1, 1, 1, 1, 1, 6, 6, 6, 19, 51, 57, 122, 122, 122, 122, 122, 1, 15, 15, 15, 15, 15, 7, 7, 1, 19, 51, 51, 57, 57, 1] 201 rigid atoms, others: [33, 2, 3, 4, 5, 6, 7, 19, 27] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32]) total number of confs: 401 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567953 none CCCN1C=NC(S(=O)(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 5, 5, 8, 1, 8, 1, 14, 11, 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, 6, 6, 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, 122, 122, 122, 122, 87, 59, 87, 87, 19, 8, 1, 1, 1, 1, 1, 1, 1, 122, 201, 201, 201, 201, 201, 186, 186, 122, 59, 19, 19, 8, 8, 122] 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: 871 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567953 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567953 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567953/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567953 Building REAL300025567954 mkdir: created directory `/scratch/stefan/7901150/working/building/REAL300025567954' /scratch/stefan/7901150/working/building/REAL300025567954 /scratch/stefan/7901150/working /scratch/stefan/7901150 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025567954 mkdir: created directory `0' /scratch/stefan/7901150/working/building/REAL300025567954/0 /scratch/stefan/7901150/working/building/REAL300025567954 /scratch/stefan/7901150/working /scratch/stefan/7901150 Protomer 0 (index: 484) Found valid previously generated 3D confromation in /scratch/stefan/7901150/working/3D/484 `/scratch/stefan/7901150/working/3D/484' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)NC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1F) `REAL300025567954.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025567954.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901150/working/building/REAL300025567954/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567954 none CS(=O)(=O)NC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 14, 11, 11, 8, 1, 1, 1, 1, 14, 11, 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, 6, 4, 7, 7, 7, 7, 7, 6, 6, 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, 11, 11, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 33, 42, 108, 108, 108, 108, 108, 1, 1, 1, 11, 11, 11, 5, 1, 1, 9, 33, 33, 42, 42, 1] 201 rigid atoms, others: [35, 4, 5, 6, 7, 8, 9, 21, 22, 23, 28, 29] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 30, 31, 32, 33, 34]) total number of confs: 309 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025567954 none CS(=O)(=O)NC1=CC=C(S(=O)(=O)NCCC2=NC(=O)O[N-]2)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 14, 11, 11, 8, 1, 1, 1, 1, 14, 11, 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, 6, 4, 7, 7, 7, 7, 7, 6, 6, 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, 191, 201, 201, 108, 108, 108, 108, 70, 52, 70, 70, 20, 8, 1, 1, 1, 1, 1, 1, 1, 108, 108, 108, 201, 201, 201, 191, 108, 108, 52, 20, 20, 8, 8, 108] 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: 698 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901150/working/building/REAL300025567954 /scratch/stefan/7901150/working /scratch/stefan/7901150 Finished preparing REAL300025567954 Recording results /scratch/stefan/7901150/working /scratch/stefan/7901150 Appending to /scratch/stefan/7901150/finished/xaaaaar_worked.* 0: /scratch/stefan/7901150/working/building/REAL300025567954/0.* Removing working files in /scratch/stefan/7901150/working/building/REAL300025567954 /scratch/stefan/7901150 Compressing combined databse files /scratch/stefan/7901150/finished/xaaaaar_worked.db2.gz /scratch/stefan/7901150/finished/xaaaaar_worked.solv.gz ======================================================= WARNING: STORE_PROTOMERS not executable or a directory! All results left in place (/scratch/stefan/7901150/finished) ======================================================= Finalizing... removed `/scratch/stefan/7901150/working/3D/485' removed directory: `/scratch/stefan/7901150/working/3D' rmdir: removing directory, `/scratch/stefan/7901150/working/building' rmdir: removing directory, `/scratch/stefan/7901150/working' ls: No match. ls: No match.