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/7901151/working' mkdir: created directory `/scratch/stefan/7901151/working/protonate' Storing results in /scratch/stefan/7901151/finished Working in /scratch/stefan/7901151/working /scratch/stefan/7901151/working /scratch/stefan/7901151 /scratch/stefan/7901151/working/protonate /scratch/stefan/7901151/working /scratch/stefan/7901151 Precomputing protomers for all compounds (pH: 7.4) ph 7.4: 117 protomers created Coalesing and merging protomers 103 protomers generated for 94 compounds Checking for new stereocenters and expanding 103 protomers after new stereo-center expansion /scratch/stefan/7901151/working /scratch/stefan/7901151 Bulk generating 3D conformations all protomers in /scratch/stefan/7901151/working/3D mkdir: created directory `/scratch/stefan/7901151/working/3D' We are using corina for 3D embeding debuging info:: /scratch/stefan/7901151/working/protonate/xaaaaat_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' 104 3D conformations generated for 94 compounds Building REAL300025569507 mkdir: created directory `/scratch/stefan/7901151/working/building' mkdir: created directory `/scratch/stefan/7901151/working/building/REAL300025569507' /scratch/stefan/7901151/working/building/REAL300025569507 /scratch/stefan/7901151/working /scratch/stefan/7901151 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025569507 mkdir: created directory `0' /scratch/stefan/7901151/working/building/REAL300025569507/0 /scratch/stefan/7901151/working/building/REAL300025569507 /scratch/stefan/7901151/working /scratch/stefan/7901151 Protomer 0 (index: 1) Found valid previously generated 3D confromation in /scratch/stefan/7901151/working/3D/1 `/scratch/stefan/7901151/working/3D/1' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)C1=CC=CC(S(=O)(=O)NCC2=NC(=O)O[N-]2)=C1) `REAL300025569507.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025569507.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901151/working/building/REAL300025569507/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569507 none CCC(=O)C1=CC=CC(S(=O)(=O)NCC2=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.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, 5, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 6, 4, 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: [28, 12, 1, 12, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 31, 107, 107, 107, 107, 107, 1, 28, 28, 28, 28, 28, 1, 1, 1, 9, 31, 31, 1] 201 rigid atoms, others: [32, 2, 4, 5, 6, 7, 8, 9, 20, 26, 27, 28] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 29, 30, 31]) total number of confs: 314 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569507 none CCC(=O)C1=CC=CC(S(=O)(=O)NCC2=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.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, 5, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 6, 4, 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, 179, 107, 179, 107, 107, 107, 107, 68, 44, 68, 68, 8, 1, 1, 1, 1, 1, 1, 1, 107, 201, 201, 201, 201, 201, 107, 107, 107, 44, 8, 8, 107] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 701 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901151/working/building/REAL300025569507 /scratch/stefan/7901151/working /scratch/stefan/7901151 Finished preparing REAL300025569507 Recording results /scratch/stefan/7901151/working /scratch/stefan/7901151 mkdir: created directory `/scratch/stefan/7901151/finished' Appending to /scratch/stefan/7901151/finished/xaaaaat_worked.* 0: /scratch/stefan/7901151/working/building/REAL300025569507/0.* Removing working files in /scratch/stefan/7901151/working/building/REAL300025569507 Building REAL300025569508 mkdir: created directory `/scratch/stefan/7901151/working/building/REAL300025569508' /scratch/stefan/7901151/working/building/REAL300025569508 /scratch/stefan/7901151/working /scratch/stefan/7901151 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025569508 mkdir: created directory `0' /scratch/stefan/7901151/working/building/REAL300025569508/0 /scratch/stefan/7901151/working/building/REAL300025569508 /scratch/stefan/7901151/working /scratch/stefan/7901151 Protomer 0 (index: 2) Found valid previously generated 3D confromation in /scratch/stefan/7901151/working/3D/2 `/scratch/stefan/7901151/working/3D/2' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN1C=C(S(=O)(=O)NCC2=NC(=O)O[N-]2)C=N1) `REAL300025569508.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025569508.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901151/working/building/REAL300025569508/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569508 none COCCN1C=C(S(=O)(=O)NCC2=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.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, 5, 5, 8, 1, 1, 14, 11, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 8, 6, 1, 1, 1, 1, 1, 2, 2, 2, 9, 33, 128, 128, 128, 128, 128, 1, 1, 18, 18, 18, 8, 8, 6, 6, 1, 9, 33, 33, 1] 201 rigid atoms, others: [3, 4, 5, 6, 7, 18, 19, 27, 31] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30]) 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: REAL300025569508 none COCCN1C=C(S(=O)(=O)NCC2=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.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, 5, 5, 8, 1, 1, 14, 11, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 6, 4, 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, 195, 128, 128, 128, 88, 48, 88, 88, 8, 1, 1, 1, 1, 1, 1, 1, 128, 128, 201, 201, 201, 201, 201, 195, 195, 128, 48, 8, 8, 128] 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: 831 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901151/working/building/REAL300025569508 /scratch/stefan/7901151/working /scratch/stefan/7901151 Finished preparing REAL300025569508 Recording results /scratch/stefan/7901151/working /scratch/stefan/7901151 Appending to /scratch/stefan/7901151/finished/xaaaaat_worked.* 0: /scratch/stefan/7901151/working/building/REAL300025569508/0.* Removing working files in /scratch/stefan/7901151/working/building/REAL300025569508 Building REAL300025569509 mkdir: created directory `/scratch/stefan/7901151/working/building/REAL300025569509' /scratch/stefan/7901151/working/building/REAL300025569509 /scratch/stefan/7901151/working /scratch/stefan/7901151 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025569509 mkdir: created directory `0' /scratch/stefan/7901151/working/building/REAL300025569509/0 /scratch/stefan/7901151/working/building/REAL300025569509 /scratch/stefan/7901151/working /scratch/stefan/7901151 Protomer 0 (index: 3) Found valid previously generated 3D confromation in /scratch/stefan/7901151/working/3D/3 `/scratch/stefan/7901151/working/3D/3' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C=C(S(=O)(=O)NCC2=NC(=O)O[N-]2)C([N+](=O)[O-])=N1) `REAL300025569509.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025569509.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901151/working/building/REAL300025569509/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569509 none CCN1C=C(S(=O)(=O)NCC2=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.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'] dock atom type numbers: [5, 5, 8, 1, 1, 14, 11, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 8, 11, 11, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 3, 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: [9, 1, 1, 1, 1, 1, 3, 3, 3, 5, 25, 105, 105, 105, 105, 105, 1, 1, 2, 2, 1, 9, 9, 9, 9, 9, 1, 5, 25, 25] 175 rigid atoms, others: [1, 2, 3, 4, 5, 16, 17, 20, 26] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 18, 19, 21, 22, 23, 24, 25, 27, 28, 29]) total number of confs: 223 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569509 none CCN1C=C(S(=O)(=O)NCC2=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.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'] dock atom type numbers: [5, 5, 8, 1, 1, 14, 11, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 8, 11, 11, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 3, 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, 105, 105, 105, 105, 57, 105, 105, 8, 1, 1, 1, 1, 1, 1, 1, 105, 105, 105, 105, 105, 175, 175, 175, 175, 175, 105, 57, 8, 8] 175 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: 811 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901151/working/building/REAL300025569509 /scratch/stefan/7901151/working /scratch/stefan/7901151 mkdir: created directory `1' /scratch/stefan/7901151/working/building/REAL300025569509/1 /scratch/stefan/7901151/working/building/REAL300025569509 /scratch/stefan/7901151/working /scratch/stefan/7901151 Protomer 1 (index: 4) Found valid previously generated 3D confromation in /scratch/stefan/7901151/working/3D/4 `/scratch/stefan/7901151/working/3D/4' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C=C(S(=O)(=O)[N-]CC2=NC(=O)O[N-]2)C([N+](=O)[O-])=N1) `REAL300025569509.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025569509.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901151/working/building/REAL300025569509/1/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: REAL300025569509 none CCN1C=C(S(=O)(=O)[N-]CC2=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.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'] dock atom type numbers: [5, 5, 8, 1, 1, 14, 11, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 8, 11, 11, 8, 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, 5, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 85 conformations in input total number of sets (complete confs): 85 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 1, 1, 1, 1, 3, 3, 3, 5, 15, 53, 53, 53, 53, 53, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 1, 15, 15] 85 rigid atoms, others: [1, 2, 3, 4, 5, 16, 17, 18, 19, 20, 26] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 27, 28]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569509 none CCN1C=C(S(=O)(=O)[N-]CC2=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.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'] dock atom type numbers: [5, 5, 8, 1, 1, 14, 11, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 8, 11, 11, 8, 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, 5, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 85 conformations in input total number of sets (complete confs): 85 using faster count positions algorithm for large data unique positions, atoms: [85, 53, 53, 53, 53, 33, 53, 53, 8, 1, 1, 1, 1, 1, 1, 1, 53, 53, 53, 53, 53, 85, 85, 85, 85, 85, 53, 8, 8] 85 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 364 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901151/working/building/REAL300025569509 /scratch/stefan/7901151/working /scratch/stefan/7901151 Finished preparing REAL300025569509 Recording results /scratch/stefan/7901151/working /scratch/stefan/7901151 Appending to /scratch/stefan/7901151/finished/xaaaaat_worked.* 0: /scratch/stefan/7901151/working/building/REAL300025569509/0.* 1: /scratch/stefan/7901151/working/building/REAL300025569509/1.* Removing working files in /scratch/stefan/7901151/working/building/REAL300025569509 Building REAL300025569510 mkdir: created directory `/scratch/stefan/7901151/working/building/REAL300025569510' /scratch/stefan/7901151/working/building/REAL300025569510 /scratch/stefan/7901151/working /scratch/stefan/7901151 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025569510 mkdir: created directory `0' /scratch/stefan/7901151/working/building/REAL300025569510/0 /scratch/stefan/7901151/working/building/REAL300025569510 /scratch/stefan/7901151/working /scratch/stefan/7901151 Protomer 0 (index: 5) Found valid previously generated 3D confromation in /scratch/stefan/7901151/working/3D/5 `/scratch/stefan/7901151/working/3D/5' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CNS(=O)(=O)C2=CC(F)=CC=C2Br)[N-]O1) `REAL300025569510.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025569510.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901151/working/building/REAL300025569510/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569510 none O=C1N=C(CNS(=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', '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'] dock atom type numbers: [11, 1, 8, 1, 5, 8, 14, 11, 11, 1, 1, 1, 15, 1, 1, 1, 17, 8, 12, 7, 7, 6, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 54 conformations in input total number of sets (complete confs): 54 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 9, 47, 54, 54, 54, 54, 54, 54, 54, 54, 54, 54, 1, 1, 9, 9, 47, 54, 54, 54] 54 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]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569510 none O=C1N=C(CNS(=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', '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'] dock atom type numbers: [11, 1, 8, 1, 5, 8, 14, 11, 11, 1, 1, 1, 15, 1, 1, 1, 17, 8, 12, 7, 7, 6, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 54 conformations in input total number of sets (complete confs): 54 using faster count positions algorithm for large data unique positions, atoms: [54, 54, 54, 25, 5, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 54, 54, 25, 25, 5, 1, 1, 1] 54 rigid atoms, others: [6, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 7, 8, 17, 18, 19, 20, 21]) total number of confs: 137 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901151/working/building/REAL300025569510 /scratch/stefan/7901151/working /scratch/stefan/7901151 Finished preparing REAL300025569510 Recording results /scratch/stefan/7901151/working /scratch/stefan/7901151 Appending to /scratch/stefan/7901151/finished/xaaaaat_worked.* 0: /scratch/stefan/7901151/working/building/REAL300025569510/0.* Removing working files in /scratch/stefan/7901151/working/building/REAL300025569510 Building REAL300025569511 mkdir: created directory `/scratch/stefan/7901151/working/building/REAL300025569511' /scratch/stefan/7901151/working/building/REAL300025569511 /scratch/stefan/7901151/working /scratch/stefan/7901151 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025569511 mkdir: created directory `0' /scratch/stefan/7901151/working/building/REAL300025569511/0 /scratch/stefan/7901151/working/building/REAL300025569511 /scratch/stefan/7901151/working /scratch/stefan/7901151 Protomer 0 (index: 6) Found valid previously generated 3D confromation in /scratch/stefan/7901151/working/3D/6 `/scratch/stefan/7901151/working/3D/6' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(S(=O)(=O)NCC2=NC(=O)O[N-]2)=C1Br) `REAL300025569511.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025569511.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901151/working/building/REAL300025569511/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569511 none CC1=CC=CC(S(=O)(=O)NCC2=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.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 17, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 60 conformations in input total number of sets (complete confs): 60 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 10, 31, 60, 60, 60, 60, 60, 1, 1, 2, 2, 2, 1, 1, 1, 10, 31, 31] 60 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 17, 18, 22, 23, 24] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 25, 26, 27]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569511 none CC1=CC=CC(S(=O)(=O)NCC2=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.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 17, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 60 conformations in input total number of sets (complete confs): 60 using faster count positions algorithm for large data unique positions, atoms: [60, 60, 60, 60, 60, 60, 45, 60, 60, 8, 1, 1, 1, 1, 1, 1, 1, 60, 60, 60, 60, 60, 60, 60, 60, 45, 8, 8] 60 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: 205 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901151/working/building/REAL300025569511 /scratch/stefan/7901151/working /scratch/stefan/7901151 Finished preparing REAL300025569511 Recording results /scratch/stefan/7901151/working /scratch/stefan/7901151 Appending to /scratch/stefan/7901151/finished/xaaaaat_worked.* 0: /scratch/stefan/7901151/working/building/REAL300025569511/0.* Removing working files in /scratch/stefan/7901151/working/building/REAL300025569511 Building REAL300025569512 mkdir: created directory `/scratch/stefan/7901151/working/building/REAL300025569512' /scratch/stefan/7901151/working/building/REAL300025569512 /scratch/stefan/7901151/working /scratch/stefan/7901151 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025569512 mkdir: created directory `0' /scratch/stefan/7901151/working/building/REAL300025569512/0 /scratch/stefan/7901151/working/building/REAL300025569512 /scratch/stefan/7901151/working /scratch/stefan/7901151 Protomer 0 (index: 7) Found valid previously generated 3D confromation in /scratch/stefan/7901151/working/3D/7 `/scratch/stefan/7901151/working/3D/7' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCCN1C=C(S(=O)(=O)NCC2=NC(=O)O[N-]2)C(=O)NC1=O) `REAL300025569512.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025569512.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901151/working/building/REAL300025569512/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569512 none CCCCCCN1C=C(S(=O)(=O)NCC2=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.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'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 8, 1, 1, 14, 11, 11, 8, 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, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 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] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 5, 5, 5, 1] 11 rigid atoms, others: [5, 38, 7, 8, 9, 42, 20, 21, 22, 23, 24, 6] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41]) total number of confs: 30 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569512 none CCCCCCN1C=C(S(=O)(=O)NCC2=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.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'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 8, 1, 1, 14, 11, 11, 8, 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, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 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] 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, 7, 7, 7, 7, 5, 7, 7, 3, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 7, 5, 3, 3, 7] 11 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: 54 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901151/working/building/REAL300025569512 /scratch/stefan/7901151/working /scratch/stefan/7901151 mkdir: created directory `1' /scratch/stefan/7901151/working/building/REAL300025569512/1 /scratch/stefan/7901151/working/building/REAL300025569512 /scratch/stefan/7901151/working /scratch/stefan/7901151 Protomer 1 (index: 8) Found valid previously generated 3D confromation in /scratch/stefan/7901151/working/3D/8 `/scratch/stefan/7901151/working/3D/8' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCCN1C=C(S(=O)(=O)[N-]CC2=NC(=O)O[N-]2)C(=O)NC1=O) `REAL300025569512.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025569512.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901151/working/building/REAL300025569512/1/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: REAL300025569512 none CCCCCCN1C=C(S(=O)(=O)[N-]CC2=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.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'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 8, 1, 1, 14, 11, 11, 8, 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, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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] 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: [19, 17, 13, 9, 5, 1, 1, 1, 1, 1, 6, 6, 6, 11, 15, 39, 39, 39, 39, 39, 1, 1, 1, 1, 1, 19, 21, 21, 21, 21, 17, 17, 13, 13, 9, 9, 5, 5, 1, 15, 15, 1] 153 rigid atoms, others: [5, 38, 7, 8, 9, 41, 20, 21, 22, 23, 24, 6] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40]) 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: REAL300025569512 none CCCCCCN1C=C(S(=O)(=O)[N-]CC2=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.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'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 8, 1, 1, 14, 11, 11, 8, 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, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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] 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: [141, 153, 119, 83, 65, 39, 39, 39, 31, 21, 31, 31, 7, 1, 1, 1, 1, 1, 1, 1, 39, 39, 39, 39, 39, 141, 153, 153, 153, 153, 153, 153, 119, 119, 83, 83, 65, 65, 39, 7, 7, 39] 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, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 725 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901151/working/building/REAL300025569512 /scratch/stefan/7901151/working /scratch/stefan/7901151 Finished preparing REAL300025569512 Recording results /scratch/stefan/7901151/working /scratch/stefan/7901151 Appending to /scratch/stefan/7901151/finished/xaaaaat_worked.* 0: /scratch/stefan/7901151/working/building/REAL300025569512/0.* 1: /scratch/stefan/7901151/working/building/REAL300025569512/1.* Removing working files in /scratch/stefan/7901151/working/building/REAL300025569512 Building REAL300025569513 mkdir: created directory `/scratch/stefan/7901151/working/building/REAL300025569513' /scratch/stefan/7901151/working/building/REAL300025569513 /scratch/stefan/7901151/working /scratch/stefan/7901151 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025569513 mkdir: created directory `0' /scratch/stefan/7901151/working/building/REAL300025569513/0 /scratch/stefan/7901151/working/building/REAL300025569513 /scratch/stefan/7901151/working /scratch/stefan/7901151 Protomer 0 (index: 9) Found valid previously generated 3D confromation in /scratch/stefan/7901151/working/3D/9 `/scratch/stefan/7901151/working/3D/9' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CNS(=O)(=O)C2=CN(C3CCOCC3)N=C2)[N-]O1) `REAL300025569513.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025569513.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901151/working/building/REAL300025569513/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569513 none O=C1N=C(CNS(=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', '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'] dock atom type numbers: [11, 1, 8, 1, 5, 8, 14, 11, 11, 1, 1, 8, 5, 5, 5, 12, 5, 5, 8, 1, 8, 12, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 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] 0 hydrogens need rotated 201 conformations in 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, 49, 77, 77, 77, 107, 107, 107, 201, 201, 201, 201, 201, 107, 107, 1, 1, 9, 9, 49, 107, 201, 201, 201, 201, 201, 201, 201, 201, 201, 107] 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]) 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569513 none O=C1N=C(CNS(=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', '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'] dock atom type numbers: [11, 1, 8, 1, 5, 8, 14, 11, 11, 1, 1, 8, 5, 5, 5, 12, 5, 5, 8, 1, 8, 12, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 119, 44, 17, 11, 17, 17, 11, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 201, 201, 119, 119, 44, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11] 201 rigid atoms, others: [32, 33, 34, 11, 12, 13, 14, 15, 16, 17, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 35]) total number of confs: 577 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569513 none O=C1N=C(CNS(=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', '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'] dock atom type numbers: [11, 1, 8, 1, 5, 8, 14, 11, 11, 1, 1, 8, 5, 5, 5, 12, 5, 5, 8, 1, 8, 12, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [107, 107, 107, 34, 9, 2, 1, 2, 2, 1, 1, 1, 1, 11, 11, 11, 11, 11, 1, 1, 107, 107, 34, 34, 9, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1] 201 rigid atoms, others: [35, 6, 9, 10, 11, 12, 18, 19, 25] set([0, 1, 2, 3, 4, 5, 7, 8, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 244 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901151/working/building/REAL300025569513 /scratch/stefan/7901151/working /scratch/stefan/7901151 Finished preparing REAL300025569513 Recording results /scratch/stefan/7901151/working /scratch/stefan/7901151 Appending to /scratch/stefan/7901151/finished/xaaaaat_worked.* 0: /scratch/stefan/7901151/working/building/REAL300025569513/0.* Removing working files in /scratch/stefan/7901151/working/building/REAL300025569513 Building REAL300025569514 mkdir: created directory `/scratch/stefan/7901151/working/building/REAL300025569514' /scratch/stefan/7901151/working/building/REAL300025569514 /scratch/stefan/7901151/working /scratch/stefan/7901151 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025569514 mkdir: created directory `0' /scratch/stefan/7901151/working/building/REAL300025569514/0 /scratch/stefan/7901151/working/building/REAL300025569514 /scratch/stefan/7901151/working /scratch/stefan/7901151 Protomer 0 (index: 10) Found valid previously generated 3D confromation in /scratch/stefan/7901151/working/3D/10 `/scratch/stefan/7901151/working/3D/10' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)S(=O)(=O)NC1=CC=C(S(=O)(=O)NCC2=NC(=O)O[N-]2)C=C1F) `REAL300025569514.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025569514.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901151/working/building/REAL300025569514/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569514 none CC(C)S(=O)(=O)NC1=CC=C(S(=O)(=O)NCC2=NC(=O)O[N-]2)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', '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.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 14, 11, 11, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 6, 4, 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 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [15, 12, 15, 7, 12, 12, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 14, 14, 14, 14, 14, 1, 1, 1, 15, 15, 15, 15, 15, 15, 15, 7, 1, 1, 5, 5, 5, 1] 21 rigid atoms, others: [33, 34, 38, 6, 7, 8, 9, 10, 11, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569514 none CC(C)S(=O)(=O)NC1=CC=C(S(=O)(=O)NCC2=NC(=O)O[N-]2)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', '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.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 14, 11, 11, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 6, 4, 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 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 21, 21, 14, 14, 14, 14, 8, 8, 8, 8, 6, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 21, 21, 21, 21, 21, 21, 21, 21, 14, 14, 8, 6, 6, 14] 21 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: 59 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901151/working/building/REAL300025569514 /scratch/stefan/7901151/working /scratch/stefan/7901151 Finished preparing REAL300025569514 Recording results /scratch/stefan/7901151/working /scratch/stefan/7901151 Appending to /scratch/stefan/7901151/finished/xaaaaat_worked.* 0: /scratch/stefan/7901151/working/building/REAL300025569514/0.* Removing working files in /scratch/stefan/7901151/working/building/REAL300025569514 Building REAL300025569515 mkdir: created directory `/scratch/stefan/7901151/working/building/REAL300025569515' /scratch/stefan/7901151/working/building/REAL300025569515 /scratch/stefan/7901151/working /scratch/stefan/7901151 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025569515 mkdir: created directory `0' /scratch/stefan/7901151/working/building/REAL300025569515/0 /scratch/stefan/7901151/working/building/REAL300025569515 /scratch/stefan/7901151/working /scratch/stefan/7901151 Protomer 0 (index: 11) Found valid previously generated 3D confromation in /scratch/stefan/7901151/working/3D/11 `/scratch/stefan/7901151/working/3D/11' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC1=CC=CC=C1)S(=O)(=O)NCC1=NC(=O)O[N-]1) `REAL300025569515.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025569515.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901151/working/building/REAL300025569515/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569515 none CCN(CC1=CC=CC=C1)S(=O)(=O)NCC1=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.2', 'N.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, 8, 5, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 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 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [9, 7, 3, 1, 1, 1, 1, 1, 1, 1, 7, 11, 11, 11, 17, 17, 23, 23, 23, 23, 23, 9, 9, 9, 9, 9, 3, 3, 1, 1, 1, 1, 1, 17, 17, 17] 23 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]) total number of confs: 86 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569515 none CCN(CC1=CC=CC=C1)S(=O)(=O)NCC1=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.2', 'N.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, 8, 5, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 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 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [19, 17, 15, 17, 17, 23, 23, 20, 23, 23, 11, 15, 15, 5, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 17, 17, 23, 23, 23, 23, 23, 11, 5, 5] 23 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: 105 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901151/working/building/REAL300025569515 /scratch/stefan/7901151/working /scratch/stefan/7901151 Finished preparing REAL300025569515 Recording results /scratch/stefan/7901151/working /scratch/stefan/7901151 Appending to /scratch/stefan/7901151/finished/xaaaaat_worked.* 0: /scratch/stefan/7901151/working/building/REAL300025569515/0.* Removing working files in /scratch/stefan/7901151/working/building/REAL300025569515 Building REAL300025569516 mkdir: created directory `/scratch/stefan/7901151/working/building/REAL300025569516' /scratch/stefan/7901151/working/building/REAL300025569516 /scratch/stefan/7901151/working /scratch/stefan/7901151 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025569516 mkdir: created directory `0' /scratch/stefan/7901151/working/building/REAL300025569516/0 /scratch/stefan/7901151/working/building/REAL300025569516 /scratch/stefan/7901151/working /scratch/stefan/7901151 Protomer 0 (index: 12) Found valid previously generated 3D confromation in /scratch/stefan/7901151/working/3D/12 `/scratch/stefan/7901151/working/3D/12' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CNS(=O)(=O)N2CCC3(CCCCC3)CC2)[N-]O1) `REAL300025569516.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025569516.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901151/working/building/REAL300025569516/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569516 none O=C1N=C(CNS(=O)(=O)N2CCC3(CCCCC3)CC2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', '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'] dock atom type numbers: [11, 1, 8, 1, 5, 8, 14, 11, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 12, 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, 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] 0 hydrogens need rotated 189 conformations in input total number of sets (complete confs): 189 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 9, 50, 135, 135, 135, 189, 189, 189, 189, 189, 189, 189, 189, 189, 189, 1, 1, 9, 9, 50, 189, 189, 189, 189, 189, 189, 189, 189, 189, 189, 189, 189, 189, 189, 189, 189, 189, 189] 189 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, 38, 39, 40, 41, 42]) 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: REAL300025569516 none O=C1N=C(CNS(=O)(=O)N2CCC3(CCCCC3)CC2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', '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'] dock atom type numbers: [11, 1, 8, 1, 5, 8, 14, 11, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 12, 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, 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] 0 hydrogens need rotated 189 conformations in input total number of sets (complete confs): 189 using faster count positions algorithm for large data unique positions, atoms: [189, 189, 189, 84, 22, 6, 1, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 189, 189, 84, 84, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 189 rigid atoms, others: [6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42] set([0, 1, 2, 3, 4, 5, 7, 8, 20, 21, 22, 23, 24]) total number of confs: 471 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901151/working/building/REAL300025569516 /scratch/stefan/7901151/working /scratch/stefan/7901151 Finished preparing REAL300025569516 Recording results /scratch/stefan/7901151/working /scratch/stefan/7901151 Appending to /scratch/stefan/7901151/finished/xaaaaat_worked.* 0: /scratch/stefan/7901151/working/building/REAL300025569516/0.* Removing working files in /scratch/stefan/7901151/working/building/REAL300025569516 Building REAL300025569517 mkdir: created directory `/scratch/stefan/7901151/working/building/REAL300025569517' /scratch/stefan/7901151/working/building/REAL300025569517 /scratch/stefan/7901151/working /scratch/stefan/7901151 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025569517 mkdir: created directory `0' /scratch/stefan/7901151/working/building/REAL300025569517/0 /scratch/stefan/7901151/working/building/REAL300025569517 /scratch/stefan/7901151/working /scratch/stefan/7901151 Protomer 0 (index: 13) Found valid previously generated 3D confromation in /scratch/stefan/7901151/working/3D/13 `/scratch/stefan/7901151/working/3D/13' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CNS(=O)(=O)C2=C(F)C=CC=C2Br)[N-]O1) `REAL300025569517.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025569517.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901151/working/building/REAL300025569517/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569517 none O=C1N=C(CNS(=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', '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'] dock atom type numbers: [11, 1, 8, 1, 5, 8, 14, 11, 11, 1, 1, 15, 1, 1, 1, 1, 17, 8, 12, 7, 7, 6, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 103 conformations in input total number of sets (complete confs): 103 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 9, 53, 86, 86, 86, 103, 103, 103, 103, 103, 103, 103, 1, 1, 9, 9, 53, 103, 103, 103] 103 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]) 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: REAL300025569517 none O=C1N=C(CNS(=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', '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'] dock atom type numbers: [11, 1, 8, 1, 5, 8, 14, 11, 11, 1, 1, 15, 1, 1, 1, 1, 17, 8, 12, 7, 7, 6, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 103 conformations in input total number of sets (complete confs): 103 using faster count positions algorithm for large data unique positions, atoms: [103, 103, 103, 49, 11, 6, 1, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 103, 103, 49, 49, 11, 1, 1, 1] 103 rigid atoms, others: [6, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 7, 8, 17, 18, 19, 20, 21]) total number of confs: 273 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901151/working/building/REAL300025569517 /scratch/stefan/7901151/working /scratch/stefan/7901151 mkdir: created directory `1' /scratch/stefan/7901151/working/building/REAL300025569517/1 /scratch/stefan/7901151/working/building/REAL300025569517 /scratch/stefan/7901151/working /scratch/stefan/7901151 Protomer 1 (index: 14) Found valid previously generated 3D confromation in /scratch/stefan/7901151/working/3D/14 `/scratch/stefan/7901151/working/3D/14' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(C[N-]S(=O)(=O)C2=C(F)C=CC=C2Br)[N-]O1) `REAL300025569517.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025569517.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901151/working/building/REAL300025569517/1/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: REAL300025569517 none O=C1N=C(C[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', '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'] dock atom type numbers: [11, 1, 8, 1, 5, 8, 14, 11, 11, 1, 1, 15, 1, 1, 1, 1, 17, 8, 12, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7] 0 hydrogens need rotated 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 9, 32, 56, 56, 56, 65, 65, 65, 56, 65, 65, 65, 1, 1, 9, 9, 65, 65, 65] 65 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]) total number of confs: 245 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569517 none O=C1N=C(C[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', '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'] dock atom type numbers: [11, 1, 8, 1, 5, 8, 14, 11, 11, 1, 1, 15, 1, 1, 1, 1, 17, 8, 12, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7] 0 hydrogens need rotated 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [65, 65, 65, 43, 16, 8, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 65, 65, 43, 43, 1, 1, 1] 65 rigid atoms, others: [6, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 7, 8, 17, 18, 19, 20]) total number of confs: 197 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901151/working/building/REAL300025569517 /scratch/stefan/7901151/working /scratch/stefan/7901151 Finished preparing REAL300025569517 Recording results /scratch/stefan/7901151/working /scratch/stefan/7901151 Appending to /scratch/stefan/7901151/finished/xaaaaat_worked.* 0: /scratch/stefan/7901151/working/building/REAL300025569517/0.* 1: /scratch/stefan/7901151/working/building/REAL300025569517/1.* Removing working files in /scratch/stefan/7901151/working/building/REAL300025569517 Building REAL300025569518 mkdir: created directory `/scratch/stefan/7901151/working/building/REAL300025569518' /scratch/stefan/7901151/working/building/REAL300025569518 /scratch/stefan/7901151/working /scratch/stefan/7901151 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025569518 mkdir: created directory `0' /scratch/stefan/7901151/working/building/REAL300025569518/0 /scratch/stefan/7901151/working/building/REAL300025569518 /scratch/stefan/7901151/working /scratch/stefan/7901151 Protomer 0 (index: 15) Found valid previously generated 3D confromation in /scratch/stefan/7901151/working/3D/15 `/scratch/stefan/7901151/working/3D/15' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CNS(=O)(=O)CC2=CC(Cl)=CC=C2F)[N-]O1) `REAL300025569518.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025569518.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901151/working/building/REAL300025569518/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569518 none O=C1N=C(CNS(=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', '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'] dock atom type numbers: [11, 1, 8, 1, 5, 8, 14, 11, 11, 5, 1, 1, 1, 16, 1, 1, 1, 15, 8, 12, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [5, 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] 0 hydrogens need rotated 201 conformations in 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, 52, 87, 87, 87, 162, 201, 201, 201, 189, 201, 201, 201, 1, 1, 9, 9, 52, 162, 162, 201, 162, 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: 843 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569518 none O=C1N=C(CNS(=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', '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'] dock atom type numbers: [11, 1, 8, 1, 5, 8, 14, 11, 11, 5, 1, 1, 1, 16, 1, 1, 1, 15, 8, 12, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [5, 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] 0 hydrogens need rotated 201 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, 51, 24, 6, 24, 24, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 121, 121, 51, 6, 6, 1, 1, 1] 201 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 626 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901151/working/building/REAL300025569518 /scratch/stefan/7901151/working /scratch/stefan/7901151 Finished preparing REAL300025569518 Recording results /scratch/stefan/7901151/working /scratch/stefan/7901151 Appending to /scratch/stefan/7901151/finished/xaaaaat_worked.* 0: /scratch/stefan/7901151/working/building/REAL300025569518/0.* Removing working files in /scratch/stefan/7901151/working/building/REAL300025569518 Building REAL300025569519 mkdir: created directory `/scratch/stefan/7901151/working/building/REAL300025569519' /scratch/stefan/7901151/working/building/REAL300025569519 /scratch/stefan/7901151/working /scratch/stefan/7901151 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025569519 mkdir: created directory `0' /scratch/stefan/7901151/working/building/REAL300025569519/0 /scratch/stefan/7901151/working/building/REAL300025569519 /scratch/stefan/7901151/working /scratch/stefan/7901151 Protomer 0 (index: 16) Found valid previously generated 3D confromation in /scratch/stefan/7901151/working/3D/16 `/scratch/stefan/7901151/working/3D/16' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CNS(=O)(=O)C2=CC3=NC=C(Cl)N=C3C=C2)[N-]O1) `REAL300025569519.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025569519.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901151/working/building/REAL300025569519/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569519 none O=C1N=C(CNS(=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', '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'] dock atom type numbers: [11, 1, 8, 1, 5, 8, 14, 11, 11, 1, 1, 1, 8, 1, 1, 16, 8, 1, 1, 1, 8, 12, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [5, 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] 0 hydrogens need rotated 97 conformations in input total number of sets (complete confs): 97 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 9, 41, 71, 71, 71, 97, 97, 97, 97, 97, 97, 97, 97, 97, 97, 1, 1, 9, 9, 41, 97, 97, 97, 97] 97 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: 334 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569519 none O=C1N=C(CNS(=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', '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'] dock atom type numbers: [11, 1, 8, 1, 5, 8, 14, 11, 11, 1, 1, 1, 8, 1, 1, 16, 8, 1, 1, 1, 8, 12, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [5, 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] 0 hydrogens need rotated 97 conformations in input total number of sets (complete confs): 97 using faster count positions algorithm for large data unique positions, atoms: [97, 97, 97, 43, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 97, 97, 43, 43, 9, 1, 1, 1, 1] 97 rigid atoms, others: [6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 7, 8, 20, 21, 22, 23, 24]) total number of confs: 231 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901151/working/building/REAL300025569519 /scratch/stefan/7901151/working /scratch/stefan/7901151 Finished preparing REAL300025569519 Recording results /scratch/stefan/7901151/working /scratch/stefan/7901151 Appending to /scratch/stefan/7901151/finished/xaaaaat_worked.* 0: /scratch/stefan/7901151/working/building/REAL300025569519/0.* Removing working files in /scratch/stefan/7901151/working/building/REAL300025569519 Building REAL300025569520 mkdir: created directory `/scratch/stefan/7901151/working/building/REAL300025569520' /scratch/stefan/7901151/working/building/REAL300025569520 /scratch/stefan/7901151/working /scratch/stefan/7901151 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025569520 mkdir: created directory `0' /scratch/stefan/7901151/working/building/REAL300025569520/0 /scratch/stefan/7901151/working/building/REAL300025569520 /scratch/stefan/7901151/working /scratch/stefan/7901151 Protomer 0 (index: 17) Found valid previously generated 3D confromation in /scratch/stefan/7901151/working/3D/17 `/scratch/stefan/7901151/working/3D/17' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CNS(=O)(=O)C2=CC=C3N=C(Cl)SC3=C2)[N-]O1) `REAL300025569520.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025569520.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901151/working/building/REAL300025569520/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569520 none O=C1N=C(CNS(=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', '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'] dock atom type numbers: [11, 1, 8, 1, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 16, 14, 1, 1, 8, 12, 7, 7, 6, 7, 7, 7] dock color type numbers: [5, 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] 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, 43, 82, 82, 82, 108, 108, 108, 108, 108, 108, 108, 108, 108, 1, 1, 9, 9, 43, 108, 108, 108] 108 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: 374 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569520 none O=C1N=C(CNS(=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', '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'] dock atom type numbers: [11, 1, 8, 1, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 16, 14, 1, 1, 8, 12, 7, 7, 6, 7, 7, 7] dock color type numbers: [5, 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] 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, 35, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 108, 108, 35, 35, 9, 1, 1, 1] 108 rigid atoms, others: [6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 7, 8, 19, 20, 21, 22, 23]) total number of confs: 234 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901151/working/building/REAL300025569520 /scratch/stefan/7901151/working /scratch/stefan/7901151 Finished preparing REAL300025569520 Recording results /scratch/stefan/7901151/working /scratch/stefan/7901151 Appending to /scratch/stefan/7901151/finished/xaaaaat_worked.* 0: /scratch/stefan/7901151/working/building/REAL300025569520/0.* Removing working files in /scratch/stefan/7901151/working/building/REAL300025569520 Building REAL300025569521 mkdir: created directory `/scratch/stefan/7901151/working/building/REAL300025569521' /scratch/stefan/7901151/working/building/REAL300025569521 /scratch/stefan/7901151/working /scratch/stefan/7901151 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025569521 mkdir: created directory `0' /scratch/stefan/7901151/working/building/REAL300025569521/0 /scratch/stefan/7901151/working/building/REAL300025569521 /scratch/stefan/7901151/working /scratch/stefan/7901151 Protomer 0 (index: 18) Found valid previously generated 3D confromation in /scratch/stefan/7901151/working/3D/18 `/scratch/stefan/7901151/working/3D/18' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C(S(=O)(=O)NCC2=NC(=O)O[N-]2)C=C1Br) `REAL300025569521.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025569521.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901151/working/building/REAL300025569521/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569521 none CCOC1=CC=C(S(=O)(=O)NCC2=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.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, 5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 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: [17, 7, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 32, 127, 127, 127, 127, 127, 1, 1, 1, 18, 18, 18, 17, 17, 1, 1, 9, 32, 32, 1] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 18, 19, 20, 26, 27, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 28, 29, 30]) total number of confs: 294 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569521 none CCOC1=CC=C(S(=O)(=O)NCC2=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.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, 5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 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, 193, 127, 127, 127, 127, 75, 45, 75, 75, 8, 1, 1, 1, 1, 1, 1, 1, 127, 127, 127, 201, 201, 201, 201, 201, 127, 127, 45, 8, 8, 127] 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: 570 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901151/working/building/REAL300025569521 /scratch/stefan/7901151/working /scratch/stefan/7901151 Finished preparing REAL300025569521 Recording results /scratch/stefan/7901151/working /scratch/stefan/7901151 Appending to /scratch/stefan/7901151/finished/xaaaaat_worked.* 0: /scratch/stefan/7901151/working/building/REAL300025569521/0.* Removing working files in /scratch/stefan/7901151/working/building/REAL300025569521 Building REAL300025569522 mkdir: created directory `/scratch/stefan/7901151/working/building/REAL300025569522' /scratch/stefan/7901151/working/building/REAL300025569522 /scratch/stefan/7901151/working /scratch/stefan/7901151 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025569522 mkdir: created directory `0' /scratch/stefan/7901151/working/building/REAL300025569522/0 /scratch/stefan/7901151/working/building/REAL300025569522 /scratch/stefan/7901151/working /scratch/stefan/7901151 Protomer 0 (index: 19) Found valid previously generated 3D confromation in /scratch/stefan/7901151/working/3D/19 `/scratch/stefan/7901151/working/3D/19' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CNS(=O)(=O)C2=CC=C(C(F)(F)F)C=C2Cl)[N-]O1) `REAL300025569522.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025569522.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901151/working/building/REAL300025569522/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569522 none O=C1N=C(CNS(=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', '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'] dock atom type numbers: [11, 1, 8, 1, 5, 8, 14, 11, 11, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 16, 8, 12, 7, 7, 6, 7, 7, 7] dock color type numbers: [5, 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] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 9, 41, 61, 61, 61, 69, 69, 69, 69, 69, 69, 69, 69, 69, 69, 1, 1, 9, 9, 41, 69, 69, 69] 69 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]) 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: REAL300025569522 none O=C1N=C(CNS(=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', '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'] dock atom type numbers: [11, 1, 8, 1, 5, 8, 14, 11, 11, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 16, 8, 12, 7, 7, 6, 7, 7, 7] dock color type numbers: [5, 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] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [69, 69, 69, 33, 9, 5, 1, 5, 5, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 69, 69, 33, 33, 9, 1, 1, 1] 69 rigid atoms, others: [6, 9, 10, 11, 12, 13, 17, 18, 19, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 7, 8, 14, 15, 16, 20, 21, 22, 23, 24]) total number of confs: 192 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901151/working/building/REAL300025569522 /scratch/stefan/7901151/working /scratch/stefan/7901151 Finished preparing REAL300025569522 Recording results /scratch/stefan/7901151/working /scratch/stefan/7901151 Appending to /scratch/stefan/7901151/finished/xaaaaat_worked.* 0: /scratch/stefan/7901151/working/building/REAL300025569522/0.* Removing working files in /scratch/stefan/7901151/working/building/REAL300025569522 Building REAL300025569523 mkdir: created directory `/scratch/stefan/7901151/working/building/REAL300025569523' /scratch/stefan/7901151/working/building/REAL300025569523 /scratch/stefan/7901151/working /scratch/stefan/7901151 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025569523 mkdir: created directory `0' /scratch/stefan/7901151/working/building/REAL300025569523/0 /scratch/stefan/7901151/working/building/REAL300025569523 /scratch/stefan/7901151/working /scratch/stefan/7901151 Protomer 0 (index: 20) Found valid previously generated 3D confromation in /scratch/stefan/7901151/working/3D/20 `/scratch/stefan/7901151/working/3D/20' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CNS(=O)(=O)C2=CC=C(Br)C(Cl)=C2)[N-]O1) `REAL300025569523.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025569523.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901151/working/building/REAL300025569523/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569523 none O=C1N=C(CNS(=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', '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'] dock atom type numbers: [11, 1, 8, 1, 5, 8, 14, 11, 11, 1, 1, 1, 1, 17, 1, 16, 1, 8, 12, 7, 7, 6, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 40, 70, 70, 70, 104, 104, 104, 104, 104, 104, 104, 1, 1, 9, 9, 40, 104, 104, 104] 104 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]) 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: REAL300025569523 none O=C1N=C(CNS(=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', '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'] dock atom type numbers: [11, 1, 8, 1, 5, 8, 14, 11, 11, 1, 1, 1, 1, 17, 1, 16, 1, 8, 12, 7, 7, 6, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 43, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 104, 104, 43, 43, 9, 1, 1, 1] 104 rigid atoms, others: [6, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 7, 8, 17, 18, 19, 20, 21]) total number of confs: 247 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901151/working/building/REAL300025569523 /scratch/stefan/7901151/working /scratch/stefan/7901151 Finished preparing REAL300025569523 Recording results /scratch/stefan/7901151/working /scratch/stefan/7901151 Appending to /scratch/stefan/7901151/finished/xaaaaat_worked.* 0: /scratch/stefan/7901151/working/building/REAL300025569523/0.* Removing working files in /scratch/stefan/7901151/working/building/REAL300025569523 Building REAL300025569524 mkdir: created directory `/scratch/stefan/7901151/working/building/REAL300025569524' /scratch/stefan/7901151/working/building/REAL300025569524 /scratch/stefan/7901151/working /scratch/stefan/7901151 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025569524 mkdir: created directory `0' /scratch/stefan/7901151/working/building/REAL300025569524/0 /scratch/stefan/7901151/working/building/REAL300025569524 /scratch/stefan/7901151/working /scratch/stefan/7901151 Protomer 0 (index: 21) Found valid previously generated 3D confromation in /scratch/stefan/7901151/working/3D/21 `/scratch/stefan/7901151/working/3D/21' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)NCC1=CC(S(=O)(=O)NCC2=NC(=O)O[N-]2)=CC=C1OC) `REAL300025569524.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025569524.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901151/working/building/REAL300025569524/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569524 none CCC(=O)NCC1=CC(S(=O)(=O)NCC2=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.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'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 1, 1, 1, 14, 11, 11, 8, 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] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [71, 19, 19, 19, 5, 1, 1, 1, 1, 1, 2, 2, 2, 7, 19, 55, 55, 55, 55, 55, 1, 1, 1, 1, 3, 71, 71, 71, 71, 71, 19, 5, 5, 1, 7, 19, 19, 1, 1, 4, 4, 4] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 20, 21, 22, 23, 38, 37] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 39, 40, 41]) 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: REAL300025569524 none CCC(=O)NCC1=CC(S(=O)(=O)NCC2=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.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'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 1, 1, 1, 14, 11, 11, 8, 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] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 143, 143, 143, 91, 55, 55, 55, 39, 25, 39, 39, 8, 1, 1, 1, 1, 1, 1, 1, 55, 55, 40, 44, 74, 201, 201, 201, 201, 201, 143, 91, 91, 55, 25, 8, 8, 55, 55, 85, 78, 76] 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: 1029 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901151/working/building/REAL300025569524 /scratch/stefan/7901151/working /scratch/stefan/7901151 Finished preparing REAL300025569524 Recording results /scratch/stefan/7901151/working /scratch/stefan/7901151 Appending to /scratch/stefan/7901151/finished/xaaaaat_worked.* 0: /scratch/stefan/7901151/working/building/REAL300025569524/0.* Removing working files in /scratch/stefan/7901151/working/building/REAL300025569524 Building REAL300025569525 mkdir: created directory `/scratch/stefan/7901151/working/building/REAL300025569525' /scratch/stefan/7901151/working/building/REAL300025569525 /scratch/stefan/7901151/working /scratch/stefan/7901151 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025569525 mkdir: created directory `0' /scratch/stefan/7901151/working/building/REAL300025569525/0 /scratch/stefan/7901151/working/building/REAL300025569525 /scratch/stefan/7901151/working /scratch/stefan/7901151 Protomer 0 (index: 22) Found valid previously generated 3D confromation in /scratch/stefan/7901151/working/3D/22 `/scratch/stefan/7901151/working/3D/22' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C1CC2=CC(S(=O)(=O)NCC3=NC(=O)O[N-]3)=CC=C2O1) `REAL300025569525.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025569525.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901151/working/building/REAL300025569525/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569525 none CCOC(=O)C1CC2=CC(S(=O)(=O)NCC3=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.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, 12, 1, 11, 5, 5, 1, 1, 1, 14, 11, 11, 8, 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] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 6, 6, 4, 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: [19, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 24, 79, 79, 79, 79, 79, 1, 1, 1, 1, 19, 19, 19, 19, 19, 1, 1, 1, 1, 8, 24, 24, 1, 1] 201 rigid atoms, others: [32, 33, 3, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 38, 37, 30, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 34, 35, 36]) total number of confs: 218 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569525 none CCOC(=O)C1CC2=CC(S(=O)(=O)NCC3=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.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, 12, 1, 11, 5, 5, 1, 1, 1, 14, 11, 11, 8, 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] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 6, 6, 4, 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, 199, 199, 79, 199, 79, 79, 79, 79, 54, 40, 54, 54, 8, 1, 1, 1, 1, 1, 1, 1, 79, 79, 79, 79, 201, 201, 201, 201, 201, 79, 79, 79, 79, 40, 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: 589 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901151/working/building/REAL300025569525 /scratch/stefan/7901151/working /scratch/stefan/7901151 Finished preparing REAL300025569525 Recording results /scratch/stefan/7901151/working /scratch/stefan/7901151 Appending to /scratch/stefan/7901151/finished/xaaaaat_worked.* 0: /scratch/stefan/7901151/working/building/REAL300025569525/0.* Removing working files in /scratch/stefan/7901151/working/building/REAL300025569525 Building REAL300025569526 mkdir: created directory `/scratch/stefan/7901151/working/building/REAL300025569526' /scratch/stefan/7901151/working/building/REAL300025569526 /scratch/stefan/7901151/working /scratch/stefan/7901151 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025569526 mkdir: created directory `0' /scratch/stefan/7901151/working/building/REAL300025569526/0 /scratch/stefan/7901151/working/building/REAL300025569526 /scratch/stefan/7901151/working /scratch/stefan/7901151 Protomer 0 (index: 23) Found valid previously generated 3D confromation in /scratch/stefan/7901151/working/3D/23 `/scratch/stefan/7901151/working/3D/23' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C1=CC=C(S(=O)(=O)NCC2=NC(=O)O[N-]2)S1) `REAL300025569526.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025569526.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901151/working/building/REAL300025569526/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569526 none CC(C)(C)C1=CC=C(S(=O)(=O)NCC2=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.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 8, 1, 11, 12, 8, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 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, 1, 4, 4, 1, 1, 1, 1, 1, 6, 6, 6, 20, 50, 117, 117, 117, 117, 117, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 20, 50, 50] 201 rigid atoms, others: [1, 4, 5, 6, 7, 8, 19, 29, 30] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 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: REAL300025569526 none CC(C)(C)C1=CC=C(S(=O)(=O)NCC2=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.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 8, 1, 11, 12, 8, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 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, 117, 201, 201, 117, 117, 117, 85, 43, 85, 85, 8, 1, 1, 1, 1, 1, 1, 1, 117, 201, 201, 201, 201, 201, 201, 201, 201, 201, 117, 117, 43, 8, 8] 201 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 898 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901151/working/building/REAL300025569526 /scratch/stefan/7901151/working /scratch/stefan/7901151 Finished preparing REAL300025569526 Recording results /scratch/stefan/7901151/working /scratch/stefan/7901151 Appending to /scratch/stefan/7901151/finished/xaaaaat_worked.* 0: /scratch/stefan/7901151/working/building/REAL300025569526/0.* Removing working files in /scratch/stefan/7901151/working/building/REAL300025569526 Building REAL300025569527 mkdir: created directory `/scratch/stefan/7901151/working/building/REAL300025569527' /scratch/stefan/7901151/working/building/REAL300025569527 /scratch/stefan/7901151/working /scratch/stefan/7901151 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025569527 mkdir: created directory `0' /scratch/stefan/7901151/working/building/REAL300025569527/0 /scratch/stefan/7901151/working/building/REAL300025569527 /scratch/stefan/7901151/working /scratch/stefan/7901151 Protomer 0 (index: 24) Found valid previously generated 3D confromation in /scratch/stefan/7901151/working/3D/24 `/scratch/stefan/7901151/working/3D/24' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CNS(=O)(=O)CC2=C(F)C=CC=C2F)[N-]O1) `REAL300025569527.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025569527.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901151/working/building/REAL300025569527/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569527 none O=C1N=C(CNS(=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', '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'] dock atom type numbers: [11, 1, 8, 1, 5, 8, 14, 11, 11, 5, 1, 1, 15, 1, 1, 1, 1, 15, 8, 12, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [5, 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] 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, 9, 57, 117, 117, 117, 182, 188, 188, 188, 188, 188, 188, 188, 1, 1, 9, 9, 57, 182, 182, 188, 188, 188] 188 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: 764 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569527 none O=C1N=C(CNS(=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', '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'] dock atom type numbers: [11, 1, 8, 1, 5, 8, 14, 11, 11, 5, 1, 1, 15, 1, 1, 1, 1, 15, 8, 12, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [5, 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] 0 hydrogens need rotated 177 conformations in input total number of sets (complete confs): 177 using faster count positions algorithm for large data unique positions, atoms: [177, 177, 177, 92, 37, 18, 4, 18, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 177, 177, 92, 92, 37, 4, 4, 1, 1, 1] 177 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 499 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901151/working/building/REAL300025569527 /scratch/stefan/7901151/working /scratch/stefan/7901151 Finished preparing REAL300025569527 Recording results /scratch/stefan/7901151/working /scratch/stefan/7901151 Appending to /scratch/stefan/7901151/finished/xaaaaat_worked.* 0: /scratch/stefan/7901151/working/building/REAL300025569527/0.* Removing working files in /scratch/stefan/7901151/working/building/REAL300025569527 Building REAL300025569528 mkdir: created directory `/scratch/stefan/7901151/working/building/REAL300025569528' /scratch/stefan/7901151/working/building/REAL300025569528 /scratch/stefan/7901151/working /scratch/stefan/7901151 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025569528 mkdir: created directory `0' /scratch/stefan/7901151/working/building/REAL300025569528/0 /scratch/stefan/7901151/working/building/REAL300025569528 /scratch/stefan/7901151/working /scratch/stefan/7901151 Protomer 0 (index: 25) Found valid previously generated 3D confromation in /scratch/stefan/7901151/working/3D/25 `/scratch/stefan/7901151/working/3D/25' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)NC1=CC=C(S(=O)(=O)NCC2=NC(=O)O[N-]2)C=C1F) `REAL300025569528.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025569528.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901151/working/building/REAL300025569528/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569528 none CS(=O)(=O)NC1=CC=C(S(=O)(=O)NCC2=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.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, 14, 11, 11, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 15, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 8, 8, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 11, 11, 11, 11, 11, 1, 1, 1, 8, 8, 8, 5, 1, 1, 5, 5, 5, 1] 20 rigid atoms, others: [32, 4, 5, 6, 7, 8, 9, 20, 21, 22, 27, 28] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 29, 30, 31]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569528 none CS(=O)(=O)NC1=CC=C(S(=O)(=O)NCC2=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.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, 14, 11, 11, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 15, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [20, 18, 20, 20, 11, 11, 11, 11, 7, 7, 7, 7, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 20, 20, 20, 18, 11, 11, 7, 5, 5, 11] 20 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: 70 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901151/working/building/REAL300025569528 /scratch/stefan/7901151/working /scratch/stefan/7901151 Finished preparing REAL300025569528 Recording results /scratch/stefan/7901151/working /scratch/stefan/7901151 Appending to /scratch/stefan/7901151/finished/xaaaaat_worked.* 0: /scratch/stefan/7901151/working/building/REAL300025569528/0.* Removing working files in /scratch/stefan/7901151/working/building/REAL300025569528 Building REAL300025569529 mkdir: created directory `/scratch/stefan/7901151/working/building/REAL300025569529' /scratch/stefan/7901151/working/building/REAL300025569529 /scratch/stefan/7901151/working /scratch/stefan/7901151 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025569529 mkdir: created directory `0' /scratch/stefan/7901151/working/building/REAL300025569529/0 /scratch/stefan/7901151/working/building/REAL300025569529 /scratch/stefan/7901151/working /scratch/stefan/7901151 Protomer 0 (index: 26) Found valid previously generated 3D confromation in /scratch/stefan/7901151/working/3D/26 `/scratch/stefan/7901151/working/3D/26' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CNS(=O)(=O)C2=C(Cl)SC(Br)=C2)[N-]O1) `REAL300025569529.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025569529.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901151/working/building/REAL300025569529/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569529 none O=C1N=C(CNS(=O)(=O)C2=C(Cl)SC(Br)=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'Br', 'C.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 8, 14, 11, 11, 1, 1, 16, 14, 1, 17, 1, 8, 12, 7, 7, 6, 7] dock color type numbers: [5, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7] 0 hydrogens need rotated 151 conformations in input total number of sets (complete confs): 151 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 9, 57, 119, 119, 119, 151, 151, 151, 151, 151, 149, 1, 1, 9, 9, 57, 151] 151 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]) 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: REAL300025569529 none O=C1N=C(CNS(=O)(=O)C2=C(Cl)SC(Br)=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'Br', 'C.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 8, 14, 11, 11, 1, 1, 16, 14, 1, 17, 1, 8, 12, 7, 7, 6, 7] dock color type numbers: [5, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7] 0 hydrogens need rotated 151 conformations in input total number of sets (complete confs): 151 using faster count positions algorithm for large data unique positions, atoms: [151, 151, 151, 78, 23, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 151, 151, 78, 78, 23, 1] 151 rigid atoms, others: [6, 9, 10, 11, 12, 13, 14, 15, 21] set([0, 1, 2, 3, 4, 5, 7, 8, 16, 17, 18, 19, 20]) total number of confs: 415 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901151/working/building/REAL300025569529 /scratch/stefan/7901151/working /scratch/stefan/7901151 mkdir: created directory `1' /scratch/stefan/7901151/working/building/REAL300025569529/1 /scratch/stefan/7901151/working/building/REAL300025569529 /scratch/stefan/7901151/working /scratch/stefan/7901151 Protomer 1 (index: 27) Found valid previously generated 3D confromation in /scratch/stefan/7901151/working/3D/27 `/scratch/stefan/7901151/working/3D/27' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(C[N-]S(=O)(=O)C2=C(Cl)SC(Br)=C2)[N-]O1) `REAL300025569529.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025569529.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901151/working/building/REAL300025569529/1/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: REAL300025569529 none O=C1N=C(C[N-]S(=O)(=O)C2=C(Cl)SC(Br)=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'Br', 'C.2', 'N.2', 'O.3', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 8, 14, 11, 11, 1, 1, 16, 14, 1, 17, 1, 8, 12, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7] 0 hydrogens need rotated 81 conformations in input total number of sets (complete confs): 81 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 9, 31, 63, 63, 63, 81, 81, 81, 81, 81, 81, 1, 1, 9, 9, 81] 81 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]) total number of confs: 254 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569529 none O=C1N=C(C[N-]S(=O)(=O)C2=C(Cl)SC(Br)=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'Br', 'C.2', 'N.2', 'O.3', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 8, 14, 11, 11, 1, 1, 16, 14, 1, 17, 1, 8, 12, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7] 0 hydrogens need rotated 81 conformations in input total number of sets (complete confs): 81 using faster count positions algorithm for large data unique positions, atoms: [81, 81, 81, 59, 21, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 81, 81, 59, 59, 1] 81 rigid atoms, others: [6, 9, 10, 11, 12, 13, 14, 15, 20] set([0, 1, 2, 3, 4, 5, 7, 8, 16, 17, 18, 19]) total number of confs: 248 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901151/working/building/REAL300025569529 /scratch/stefan/7901151/working /scratch/stefan/7901151 Finished preparing REAL300025569529 Recording results /scratch/stefan/7901151/working /scratch/stefan/7901151 Appending to /scratch/stefan/7901151/finished/xaaaaat_worked.* 0: /scratch/stefan/7901151/working/building/REAL300025569529/0.* 1: /scratch/stefan/7901151/working/building/REAL300025569529/1.* Removing working files in /scratch/stefan/7901151/working/building/REAL300025569529 Building REAL300025569530 mkdir: created directory `/scratch/stefan/7901151/working/building/REAL300025569530' /scratch/stefan/7901151/working/building/REAL300025569530 /scratch/stefan/7901151/working /scratch/stefan/7901151 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025569530 mkdir: created directory `0' /scratch/stefan/7901151/working/building/REAL300025569530/0 /scratch/stefan/7901151/working/building/REAL300025569530 /scratch/stefan/7901151/working /scratch/stefan/7901151 Protomer 0 (index: 28) Found valid previously generated 3D confromation in /scratch/stefan/7901151/working/3D/28 `/scratch/stefan/7901151/working/3D/28' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CNS(=O)(=O)C2=CN(C3CCOC3)N=C2)[N-]O1) `REAL300025569530.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025569530.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901151/working/building/REAL300025569530/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569530 none O=C1N=C(CNS(=O)(=O)C2=CN(C3CCOC3)N=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', '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', '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, 8, 14, 11, 11, 1, 1, 8, 5, 5, 5, 12, 5, 8, 1, 8, 12, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 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, 7] 0 hydrogens need rotated 201 conformations in 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, 43, 70, 70, 70, 94, 94, 94, 201, 201, 201, 201, 94, 94, 1, 1, 9, 9, 43, 94, 201, 201, 201, 201, 201, 201, 201, 94] 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: 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569530 none O=C1N=C(CNS(=O)(=O)C2=CN(C3CCOC3)N=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', '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', '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, 8, 14, 11, 11, 1, 1, 8, 5, 5, 5, 12, 5, 8, 1, 8, 12, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 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, 7] 0 hydrogens need rotated 201 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, 41, 16, 9, 16, 16, 9, 9, 1, 1, 1, 1, 1, 1, 9, 9, 201, 201, 107, 107, 41, 9, 1, 1, 1, 1, 1, 1, 1, 9] 201 rigid atoms, others: [11, 12, 13, 14, 15, 16, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 24, 32]) total number of confs: 550 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569530 none O=C1N=C(CNS(=O)(=O)C2=CN(C3CCOC3)N=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', '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', '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, 8, 14, 11, 11, 1, 1, 8, 5, 5, 5, 12, 5, 8, 1, 8, 12, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 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, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [94, 94, 94, 35, 9, 2, 1, 2, 2, 1, 1, 1, 1, 9, 9, 9, 9, 1, 1, 94, 94, 35, 35, 9, 1, 9, 9, 9, 9, 9, 9, 9, 1] 201 rigid atoms, others: [32, 6, 9, 10, 11, 12, 17, 18, 24] set([0, 1, 2, 3, 4, 5, 7, 8, 13, 14, 15, 16, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 231 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901151/working/building/REAL300025569530 /scratch/stefan/7901151/working /scratch/stefan/7901151 Finished preparing REAL300025569530 Recording results /scratch/stefan/7901151/working /scratch/stefan/7901151 Appending to /scratch/stefan/7901151/finished/xaaaaat_worked.* 0: /scratch/stefan/7901151/working/building/REAL300025569530/0.* Removing working files in /scratch/stefan/7901151/working/building/REAL300025569530 Building REAL300025569531 mkdir: created directory `/scratch/stefan/7901151/working/building/REAL300025569531' /scratch/stefan/7901151/working/building/REAL300025569531 /scratch/stefan/7901151/working /scratch/stefan/7901151 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025569531 mkdir: created directory `0' /scratch/stefan/7901151/working/building/REAL300025569531/0 /scratch/stefan/7901151/working/building/REAL300025569531 /scratch/stefan/7901151/working /scratch/stefan/7901151 Protomer 0 (index: 29) Found valid previously generated 3D confromation in /scratch/stefan/7901151/working/3D/29 `/scratch/stefan/7901151/working/3D/29' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(C1CCCC1)N1CCCC(S(=O)(=O)NCC2=NC(=O)O[N-]2)C1) `REAL300025569531.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025569531.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901151/working/building/REAL300025569531/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569531 none O=C(C1CCCC1)N1CCCC(S(=O)(=O)NCC2=NC(=O)O[N-]2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 8, 5, 5, 5, 5, 14, 11, 11, 8, 5, 1, 8, 1, 11, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 1, 1, 1, 1, 1, 6, 16, 16, 16, 16, 16, 51, 51, 51, 80, 130, 201, 201, 201, 201, 201, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 16, 16, 80, 130, 130, 16, 16] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 661 number of broken/clashed sets: 55 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569531 none O=C(C1CCCC1)N1CCCC(S(=O)(=O)NCC2=NC(=O)O[N-]2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 8, 5, 5, 5, 5, 14, 11, 11, 8, 5, 1, 8, 1, 11, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [163, 91, 163, 201, 201, 201, 201, 91, 91, 91, 91, 70, 42, 70, 70, 8, 1, 1, 1, 1, 1, 1, 1, 91, 201, 201, 201, 201, 201, 201, 201, 201, 201, 91, 91, 91, 91, 91, 91, 91, 42, 8, 8, 91, 91] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 707 number of broken/clashed sets: 55 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569531 none O=C(C1CCCC1)N1CCCC(S(=O)(=O)NCC2=NC(=O)O[N-]2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 8, 5, 5, 5, 5, 14, 11, 11, 8, 5, 1, 8, 1, 11, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 16, 16, 16, 16, 1, 1, 1, 1, 1, 1, 6, 6, 6, 15, 33, 91, 91, 91, 91, 91, 1, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1, 1, 1, 1, 1, 1, 1, 15, 33, 33, 1, 1] 201 rigid atoms, others: [1, 34, 35, 36, 37, 38, 33, 8, 9, 10, 7, 12, 44, 11, 43, 23, 39] set([0, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42]) total number of confs: 250 number of broken/clashed sets: 55 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901151/working/building/REAL300025569531 /scratch/stefan/7901151/working /scratch/stefan/7901151 Finished preparing REAL300025569531 Recording results /scratch/stefan/7901151/working /scratch/stefan/7901151 Appending to /scratch/stefan/7901151/finished/xaaaaat_worked.* 0: /scratch/stefan/7901151/working/building/REAL300025569531/0.* Removing working files in /scratch/stefan/7901151/working/building/REAL300025569531 Building REAL300025569532 mkdir: created directory `/scratch/stefan/7901151/working/building/REAL300025569532' /scratch/stefan/7901151/working/building/REAL300025569532 /scratch/stefan/7901151/working /scratch/stefan/7901151 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025569532 mkdir: created directory `0' /scratch/stefan/7901151/working/building/REAL300025569532/0 /scratch/stefan/7901151/working/building/REAL300025569532 /scratch/stefan/7901151/working /scratch/stefan/7901151 Protomer 0 (index: 30) Found valid previously generated 3D confromation in /scratch/stefan/7901151/working/3D/30 `/scratch/stefan/7901151/working/3D/30' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C1=CC(F)=C(OC)C(S(=O)(=O)NCC2=NC(=O)O[N-]2)=C1) `REAL300025569532.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025569532.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901151/working/building/REAL300025569532/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569532 none CCOC(=O)C1=CC(F)=C(OC)C(S(=O)(=O)NCC2=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', 'F', 'C.ar', 'O.3', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 5, 12, 1, 11, 1, 1, 1, 15, 1, 12, 5, 1, 14, 11, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 6, 4, 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: [45, 21, 11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 15, 17, 49, 49, 49, 49, 49, 1, 45, 45, 45, 45, 45, 1, 5, 5, 5, 15, 17, 17, 1] 201 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 12, 13, 24, 30, 37] set([0, 1, 2, 4, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36]) total number of confs: 260 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569532 none CCOC(=O)C1=CC(F)=C(OC)C(S(=O)(=O)NCC2=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', 'F', 'C.ar', 'O.3', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 5, 12, 1, 11, 1, 1, 1, 15, 1, 12, 5, 1, 14, 11, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 6, 4, 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, 159, 146, 49, 146, 49, 49, 49, 49, 49, 49, 84, 27, 17, 27, 27, 7, 1, 1, 1, 1, 1, 1, 1, 49, 201, 201, 201, 201, 201, 49, 84, 84, 84, 17, 7, 7, 49] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 727 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901151/working/building/REAL300025569532 /scratch/stefan/7901151/working /scratch/stefan/7901151 Finished preparing REAL300025569532 Recording results /scratch/stefan/7901151/working /scratch/stefan/7901151 Appending to /scratch/stefan/7901151/finished/xaaaaat_worked.* 0: /scratch/stefan/7901151/working/building/REAL300025569532/0.* Removing working files in /scratch/stefan/7901151/working/building/REAL300025569532 Building REAL300025569533 mkdir: created directory `/scratch/stefan/7901151/working/building/REAL300025569533' /scratch/stefan/7901151/working/building/REAL300025569533 /scratch/stefan/7901151/working /scratch/stefan/7901151 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025569533 mkdir: created directory `0' /scratch/stefan/7901151/working/building/REAL300025569533/0 /scratch/stefan/7901151/working/building/REAL300025569533 /scratch/stefan/7901151/working /scratch/stefan/7901151 Protomer 0 (index: 31) Found valid previously generated 3D confromation in /scratch/stefan/7901151/working/3D/31 `/scratch/stefan/7901151/working/3D/31' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC([N+](=O)[O-])=CC=C1S(=O)(=O)NCC1=NC(=O)O[N-]1) `REAL300025569533.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025569533.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901151/working/building/REAL300025569533/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569533 none COC(=O)C1=CC([N+](=O)[O-])=CC=C1S(=O)(=O)NCC1=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', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 1, 1, 8, 11, 11, 1, 1, 1, 14, 11, 11, 8, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 6, 6, 4, 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: [9, 9, 1, 9, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 5, 5, 11, 45, 145, 145, 145, 145, 145, 9, 9, 9, 1, 1, 1, 11, 45, 45] 201 rigid atoms, others: [2, 4, 5, 6, 7, 10, 11, 12, 13, 27, 28, 29] set([0, 1, 3, 32, 8, 9, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 326 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569533 none COC(=O)C1=CC([N+](=O)[O-])=CC=C1S(=O)(=O)NCC1=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', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 1, 1, 8, 11, 11, 1, 1, 1, 14, 11, 11, 8, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 6, 6, 4, 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, 145, 201, 145, 145, 113, 145, 145, 145, 145, 145, 110, 57, 110, 110, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 145, 145, 145, 57, 8, 8] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 868 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901151/working/building/REAL300025569533 /scratch/stefan/7901151/working /scratch/stefan/7901151 Finished preparing REAL300025569533 Recording results /scratch/stefan/7901151/working /scratch/stefan/7901151 Appending to /scratch/stefan/7901151/finished/xaaaaat_worked.* 0: /scratch/stefan/7901151/working/building/REAL300025569533/0.* Removing working files in /scratch/stefan/7901151/working/building/REAL300025569533 Building REAL300025569534 mkdir: created directory `/scratch/stefan/7901151/working/building/REAL300025569534' /scratch/stefan/7901151/working/building/REAL300025569534 /scratch/stefan/7901151/working /scratch/stefan/7901151 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025569534 mkdir: created directory `0' /scratch/stefan/7901151/working/building/REAL300025569534/0 /scratch/stefan/7901151/working/building/REAL300025569534 /scratch/stefan/7901151/working /scratch/stefan/7901151 Protomer 0 (index: 32) Found valid previously generated 3D confromation in /scratch/stefan/7901151/working/3D/32 `/scratch/stefan/7901151/working/3D/32' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C(S(=O)(=O)NCC2=NC(=O)O[N-]2)C=N1) `REAL300025569534.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025569534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901151/working/building/REAL300025569534/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569534 none CCOC1=CC=C(S(=O)(=O)NCC2=NC(=O)O[N-]2)C=N1 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.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, 5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 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: [11, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 35, 146, 146, 146, 146, 146, 1, 1, 12, 12, 12, 11, 11, 1, 1, 9, 35, 35, 1] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 18, 19, 25, 26, 30] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 27, 28, 29]) 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: REAL300025569534 none CCOC1=CC=C(S(=O)(=O)NCC2=NC(=O)O[N-]2)C=N1 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.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, 5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 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, 157, 146, 146, 146, 146, 84, 47, 84, 84, 8, 1, 1, 1, 1, 1, 1, 1, 146, 146, 201, 201, 201, 201, 201, 146, 146, 47, 8, 8, 146] 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: 739 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901151/working/building/REAL300025569534 /scratch/stefan/7901151/working /scratch/stefan/7901151 Finished preparing REAL300025569534 Recording results /scratch/stefan/7901151/working /scratch/stefan/7901151 Appending to /scratch/stefan/7901151/finished/xaaaaat_worked.* 0: /scratch/stefan/7901151/working/building/REAL300025569534/0.* Removing working files in /scratch/stefan/7901151/working/building/REAL300025569534 Building REAL300025569535 mkdir: created directory `/scratch/stefan/7901151/working/building/REAL300025569535' /scratch/stefan/7901151/working/building/REAL300025569535 /scratch/stefan/7901151/working /scratch/stefan/7901151 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025569535 mkdir: created directory `0' /scratch/stefan/7901151/working/building/REAL300025569535/0 /scratch/stefan/7901151/working/building/REAL300025569535 /scratch/stefan/7901151/working /scratch/stefan/7901151 Protomer 0 (index: 33) Found valid previously generated 3D confromation in /scratch/stefan/7901151/working/3D/33 `/scratch/stefan/7901151/working/3D/33' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC1=CC=C(S(=O)(=O)NCC2=NC(=O)O[N-]2)C=C1) `REAL300025569535.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025569535.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901151/working/building/REAL300025569535/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569535 none CC(=O)NC1=CC=C(S(=O)(=O)NCC2=NC(=O)O[N-]2)C=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.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 152 conformations in input total number of sets (complete confs): 152 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 41, 120, 120, 120, 120, 120, 1, 1, 3, 3, 3, 3, 1, 1, 9, 41, 41, 1, 1] 152 rigid atoms, others: [3, 4, 5, 6, 7, 8, 19, 20, 25, 26, 30, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 27, 28, 29]) 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: REAL300025569535 none CC(=O)NC1=CC=C(S(=O)(=O)NCC2=NC(=O)O[N-]2)C=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.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 152 conformations in input total number of sets (complete confs): 152 using faster count positions algorithm for large data unique positions, atoms: [152, 152, 152, 120, 120, 120, 120, 88, 47, 88, 88, 8, 1, 1, 1, 1, 1, 1, 1, 120, 120, 152, 152, 152, 152, 120, 120, 47, 8, 8, 120, 120] 152 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: 536 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901151/working/building/REAL300025569535 /scratch/stefan/7901151/working /scratch/stefan/7901151 Finished preparing REAL300025569535 Recording results /scratch/stefan/7901151/working /scratch/stefan/7901151 Appending to /scratch/stefan/7901151/finished/xaaaaat_worked.* 0: /scratch/stefan/7901151/working/building/REAL300025569535/0.* Removing working files in /scratch/stefan/7901151/working/building/REAL300025569535 Building REAL300025569536 mkdir: created directory `/scratch/stefan/7901151/working/building/REAL300025569536' /scratch/stefan/7901151/working/building/REAL300025569536 /scratch/stefan/7901151/working /scratch/stefan/7901151 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025569536 mkdir: created directory `0' /scratch/stefan/7901151/working/building/REAL300025569536/0 /scratch/stefan/7901151/working/building/REAL300025569536 /scratch/stefan/7901151/working /scratch/stefan/7901151 Protomer 0 (index: 34) Found valid previously generated 3D confromation in /scratch/stefan/7901151/working/3D/34 `/scratch/stefan/7901151/working/3D/34' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(S(=O)(=O)NCC2=NC(=O)O[N-]2)=C1Cl) `REAL300025569536.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025569536.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901151/working/building/REAL300025569536/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569536 none CC1=CC=CC(S(=O)(=O)NCC2=NC(=O)O[N-]2)=C1Cl 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.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 16, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 85 conformations in input total number of sets (complete confs): 85 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 13, 41, 85, 85, 85, 85, 85, 1, 1, 2, 2, 2, 1, 1, 1, 13, 41, 41] 85 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 17, 18, 22, 23, 24] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 25, 26, 27]) total number of confs: 226 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569536 none CC1=CC=CC(S(=O)(=O)NCC2=NC(=O)O[N-]2)=C1Cl 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.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 16, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 85 conformations in input total number of sets (complete confs): 85 using faster count positions algorithm for large data unique positions, atoms: [85, 85, 85, 85, 85, 77, 49, 77, 77, 8, 1, 1, 1, 1, 1, 1, 1, 85, 85, 85, 85, 85, 85, 85, 85, 49, 8, 8] 85 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: 289 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901151/working/building/REAL300025569536 /scratch/stefan/7901151/working /scratch/stefan/7901151 Finished preparing REAL300025569536 Recording results /scratch/stefan/7901151/working /scratch/stefan/7901151 Appending to /scratch/stefan/7901151/finished/xaaaaat_worked.* 0: /scratch/stefan/7901151/working/building/REAL300025569536/0.* Removing working files in /scratch/stefan/7901151/working/building/REAL300025569536 Building REAL300025569537 mkdir: created directory `/scratch/stefan/7901151/working/building/REAL300025569537' /scratch/stefan/7901151/working/building/REAL300025569537 /scratch/stefan/7901151/working /scratch/stefan/7901151 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025569537 mkdir: created directory `0' /scratch/stefan/7901151/working/building/REAL300025569537/0 /scratch/stefan/7901151/working/building/REAL300025569537 /scratch/stefan/7901151/working /scratch/stefan/7901151 Protomer 0 (index: 35) Found valid previously generated 3D confromation in /scratch/stefan/7901151/working/3D/35 `/scratch/stefan/7901151/working/3D/35' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)C1=CC(S(=O)(=O)NCC2=NC(=O)O[N-]2)=CC=C1Br) `REAL300025569537.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025569537.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901151/working/building/REAL300025569537/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569537 none CC(=O)C1=CC(S(=O)(=O)NCC2=NC(=O)O[N-]2)=CC=C1Br NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [5, 1, 11, 1, 1, 1, 14, 11, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 17, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 178 conformations in input total number of sets (complete confs): 178 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 1, 1, 1, 1, 3, 3, 3, 9, 33, 137, 137, 137, 137, 137, 1, 1, 1, 1, 7, 7, 7, 1, 9, 33, 33, 1, 1] 178 rigid atoms, others: [1, 3, 4, 5, 6, 17, 18, 19, 20, 24, 28, 29] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 25, 26, 27]) total number of confs: 271 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569537 none CC(=O)C1=CC(S(=O)(=O)NCC2=NC(=O)O[N-]2)=CC=C1Br NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [5, 1, 11, 1, 1, 1, 14, 11, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 17, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 178 conformations in input total number of sets (complete confs): 178 using faster count positions algorithm for large data unique positions, atoms: [178, 137, 178, 137, 137, 88, 49, 88, 88, 8, 1, 1, 1, 1, 1, 1, 1, 137, 137, 137, 137, 178, 178, 178, 137, 49, 8, 8, 137, 137] 178 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 607 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901151/working/building/REAL300025569537 /scratch/stefan/7901151/working /scratch/stefan/7901151 Finished preparing REAL300025569537 Recording results /scratch/stefan/7901151/working /scratch/stefan/7901151 Appending to /scratch/stefan/7901151/finished/xaaaaat_worked.* 0: /scratch/stefan/7901151/working/building/REAL300025569537/0.* Removing working files in /scratch/stefan/7901151/working/building/REAL300025569537 Building REAL300025569538 mkdir: created directory `/scratch/stefan/7901151/working/building/REAL300025569538' /scratch/stefan/7901151/working/building/REAL300025569538 /scratch/stefan/7901151/working /scratch/stefan/7901151 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025569538 mkdir: created directory `0' /scratch/stefan/7901151/working/building/REAL300025569538/0 /scratch/stefan/7901151/working/building/REAL300025569538 /scratch/stefan/7901151/working /scratch/stefan/7901151 Protomer 0 (index: 36) Found valid previously generated 3D confromation in /scratch/stefan/7901151/working/3D/36 `/scratch/stefan/7901151/working/3D/36' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=C(S(=O)(=O)NCC2=NC(=O)O[N-]2)C=C1C(=O)NCC(F)(F)F) `REAL300025569538.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025569538.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901151/working/building/REAL300025569538/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569538 none CN1C=C(S(=O)(=O)NCC2=NC(=O)O[N-]2)C=C1C(=O)NCC(F)(F)F 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.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 11, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 11, 8, 5, 5, 15, 15, 15, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in 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, 32, 104, 104, 104, 104, 104, 1, 1, 1, 8, 8, 8, 22, 22, 22, 22, 2, 2, 2, 1, 9, 32, 32, 1, 8, 22, 22] 201 rigid atoms, others: [0, 1, 2, 3, 4, 32, 15, 16, 17, 28] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 33, 34, 35]) total number of confs: 286 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569538 none CN1C=C(S(=O)(=O)NCC2=NC(=O)O[N-]2)C=C1C(=O)NCC(F)(F)F 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.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 11, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 11, 8, 5, 5, 15, 15, 15, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [104, 104, 104, 72, 47, 72, 72, 8, 1, 1, 1, 1, 1, 1, 1, 104, 104, 104, 122, 122, 122, 201, 201, 201, 201, 104, 104, 104, 104, 47, 8, 8, 104, 122, 201, 201] 201 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 756 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901151/working/building/REAL300025569538 /scratch/stefan/7901151/working /scratch/stefan/7901151 Finished preparing REAL300025569538 Recording results /scratch/stefan/7901151/working /scratch/stefan/7901151 Appending to /scratch/stefan/7901151/finished/xaaaaat_worked.* 0: /scratch/stefan/7901151/working/building/REAL300025569538/0.* Removing working files in /scratch/stefan/7901151/working/building/REAL300025569538 Building REAL300025569539 mkdir: created directory `/scratch/stefan/7901151/working/building/REAL300025569539' /scratch/stefan/7901151/working/building/REAL300025569539 /scratch/stefan/7901151/working /scratch/stefan/7901151 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025569539 mkdir: created directory `0' /scratch/stefan/7901151/working/building/REAL300025569539/0 /scratch/stefan/7901151/working/building/REAL300025569539 /scratch/stefan/7901151/working /scratch/stefan/7901151 Protomer 0 (index: 37) Found valid previously generated 3D confromation in /scratch/stefan/7901151/working/3D/37 `/scratch/stefan/7901151/working/3D/37' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)CC1=CC=C(Cl)C=C1S(=O)(=O)NCC1=NC(=O)O[N-]1) `REAL300025569539.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025569539.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901151/working/building/REAL300025569539/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569539 none CS(=O)(=O)CC1=CC=C(Cl)C=C1S(=O)(=O)NCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', '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.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 5, 1, 1, 1, 1, 16, 1, 1, 14, 11, 11, 8, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 5, 3, 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: [10, 6, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 25, 80, 80, 80, 80, 80, 10, 10, 10, 6, 6, 1, 1, 1, 7, 25, 25] 100 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 12, 28, 29, 30] set([0, 1, 2, 3, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569539 none CS(=O)(=O)CC1=CC=C(Cl)C=C1S(=O)(=O)NCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', '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.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 5, 1, 1, 1, 1, 16, 1, 1, 14, 11, 11, 8, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 5, 3, 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, 99, 100, 100, 80, 80, 80, 80, 80, 80, 80, 74, 43, 74, 74, 8, 1, 1, 1, 1, 1, 1, 1, 100, 100, 100, 99, 99, 80, 80, 80, 43, 8, 8] 100 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: 411 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901151/working/building/REAL300025569539 /scratch/stefan/7901151/working /scratch/stefan/7901151 Finished preparing REAL300025569539 Recording results /scratch/stefan/7901151/working /scratch/stefan/7901151 Appending to /scratch/stefan/7901151/finished/xaaaaat_worked.* 0: /scratch/stefan/7901151/working/building/REAL300025569539/0.* Removing working files in /scratch/stefan/7901151/working/building/REAL300025569539 Building REAL300025569540 mkdir: created directory `/scratch/stefan/7901151/working/building/REAL300025569540' /scratch/stefan/7901151/working/building/REAL300025569540 /scratch/stefan/7901151/working /scratch/stefan/7901151 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025569540 mkdir: created directory `0' /scratch/stefan/7901151/working/building/REAL300025569540/0 /scratch/stefan/7901151/working/building/REAL300025569540 /scratch/stefan/7901151/working /scratch/stefan/7901151 Protomer 0 (index: 38) Found valid previously generated 3D confromation in /scratch/stefan/7901151/working/3D/38 `/scratch/stefan/7901151/working/3D/38' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1=NC(=O)O[N-]1)N(C1=CC=CC=C1)C1=CC=CC=C1) `REAL300025569540.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025569540.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901151/working/building/REAL300025569540/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569540 none O=C(NCC1=NC(=O)O[N-]1)N(C1=CC=CC=C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 11, 12, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [44, 43, 8, 1, 1, 1, 1, 1, 1, 1, 44, 73, 73, 73, 73, 73, 73, 73, 73, 73, 73, 73, 73, 43, 8, 8, 73, 73, 73, 73, 73, 73, 73, 73, 73, 73] 73 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569540 none O=C(NCC1=NC(=O)O[N-]1)N(C1=CC=CC=C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 11, 12, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 74 conformations in input total number of sets (complete confs): 74 using faster count positions algorithm for large data unique positions, atoms: [11, 5, 11, 11, 32, 74, 74, 74, 74, 74, 1, 5, 8, 8, 5, 8, 8, 1, 1, 1, 1, 1, 1, 11, 32, 32, 8, 8, 7, 8, 8, 1, 1, 1, 1, 1] 74 rigid atoms, others: [32, 33, 34, 35, 10, 17, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 200 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569540 none O=C(NCC1=NC(=O)O[N-]1)N(C1=CC=CC=C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 11, 12, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 74 conformations in input total number of sets (complete confs): 74 using faster count positions algorithm for large data unique positions, atoms: [14, 4, 14, 14, 33, 74, 74, 74, 74, 74, 1, 1, 1, 1, 1, 1, 1, 4, 8, 8, 4, 8, 8, 14, 33, 33, 1, 1, 1, 1, 1, 8, 8, 5, 8, 8] 74 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 31, 32, 33, 34, 35]) total number of confs: 197 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901151/working/building/REAL300025569540 /scratch/stefan/7901151/working /scratch/stefan/7901151 Finished preparing REAL300025569540 Recording results /scratch/stefan/7901151/working /scratch/stefan/7901151 Appending to /scratch/stefan/7901151/finished/xaaaaat_worked.* 0: /scratch/stefan/7901151/working/building/REAL300025569540/0.* Removing working files in /scratch/stefan/7901151/working/building/REAL300025569540 Building REAL300025569541 mkdir: created directory `/scratch/stefan/7901151/working/building/REAL300025569541' /scratch/stefan/7901151/working/building/REAL300025569541 /scratch/stefan/7901151/working /scratch/stefan/7901151 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025569541 mkdir: created directory `0' /scratch/stefan/7901151/working/building/REAL300025569541/0 /scratch/stefan/7901151/working/building/REAL300025569541 /scratch/stefan/7901151/working /scratch/stefan/7901151 Protomer 0 (index: 39) Found valid previously generated 3D confromation in /scratch/stefan/7901151/working/3D/39 `/scratch/stefan/7901151/working/3D/39' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CNS(=O)(=O)C2=C3NC(=O)COC3=CC=C2)[N-]O1) `REAL300025569541.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025569541.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901151/working/building/REAL300025569541/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569541 none O=C1N=C(CNS(=O)(=O)C2=C3NC(=O)COC3=CC=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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, 8, 14, 11, 11, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 12, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 3, 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, 9, 53, 98, 98, 98, 143, 143, 143, 143, 143, 143, 143, 143, 143, 143, 1, 1, 9, 9, 53, 143, 143, 143, 143, 143, 143] 143 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: 451 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569541 none O=C1N=C(CNS(=O)(=O)C2=C3NC(=O)COC3=CC=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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, 8, 14, 11, 11, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 12, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 3, 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, 143, 143, 70, 21, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 143, 143, 70, 70, 21, 1, 1, 1, 1, 1, 1] 143 rigid atoms, others: [6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 7, 8, 20, 21, 22, 23, 24]) total number of confs: 378 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901151/working/building/REAL300025569541 /scratch/stefan/7901151/working /scratch/stefan/7901151 Finished preparing REAL300025569541 Recording results /scratch/stefan/7901151/working /scratch/stefan/7901151 Appending to /scratch/stefan/7901151/finished/xaaaaat_worked.* 0: /scratch/stefan/7901151/working/building/REAL300025569541/0.* Removing working files in /scratch/stefan/7901151/working/building/REAL300025569541 Building REAL300025569542 mkdir: created directory `/scratch/stefan/7901151/working/building/REAL300025569542' /scratch/stefan/7901151/working/building/REAL300025569542 /scratch/stefan/7901151/working /scratch/stefan/7901151 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025569542 mkdir: created directory `0' /scratch/stefan/7901151/working/building/REAL300025569542/0 /scratch/stefan/7901151/working/building/REAL300025569542 /scratch/stefan/7901151/working /scratch/stefan/7901151 Protomer 0 (index: 40) Found valid previously generated 3D confromation in /scratch/stefan/7901151/working/3D/40 `/scratch/stefan/7901151/working/3D/40' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1(C2=CC=C(S(=O)(=O)NCC3=NC(=O)O[N-]3)C=C2)CC1) `REAL300025569542.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025569542.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901151/working/building/REAL300025569542/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569542 none COC(=O)C1(C2=CC=C(S(=O)(=O)NCC3=NC(=O)O[N-]3)C=C2)CC1 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.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'] dock atom type numbers: [5, 12, 1, 11, 5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 5, 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, 7, 6, 6, 4, 7, 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 99 conformations in input total number of sets (complete confs): 99 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 1, 13, 1, 1, 4, 4, 4, 4, 5, 5, 5, 13, 15, 49, 49, 49, 49, 49, 4, 4, 1, 1, 13, 13, 13, 4, 4, 13, 15, 15, 4, 4, 1, 1, 1, 1] 99 rigid atoms, others: [2, 35, 4, 5, 34, 22, 23, 36, 37] set([0, 1, 3, 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: 121 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569542 none COC(=O)C1(C2=CC=C(S(=O)(=O)NCC3=NC(=O)O[N-]3)C=C2)CC1 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.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'] dock atom type numbers: [5, 12, 1, 11, 5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 5, 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, 7, 6, 6, 4, 7, 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 99 conformations in input total number of sets (complete confs): 99 using faster count positions algorithm for large data unique positions, atoms: [99, 99, 49, 99, 37, 29, 37, 37, 29, 23, 29, 29, 8, 1, 1, 1, 1, 1, 1, 1, 37, 37, 49, 49, 99, 99, 99, 37, 37, 23, 8, 8, 37, 37, 49, 49, 49, 49] 99 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: 381 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569542 none COC(=O)C1(C2=CC=C(S(=O)(=O)NCC3=NC(=O)O[N-]3)C=C2)CC1 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.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'] dock atom type numbers: [5, 12, 1, 11, 5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 5, 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, 7, 6, 6, 4, 7, 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 99 conformations in input total number of sets (complete confs): 99 using faster count positions algorithm for large data unique positions, atoms: [30, 30, 4, 30, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 10, 37, 37, 37, 37, 37, 1, 1, 4, 4, 30, 30, 30, 1, 1, 8, 10, 10, 1, 1, 4, 4, 4, 4] 99 rigid atoms, others: [32, 33, 4, 5, 6, 7, 8, 9, 20, 21, 27, 28] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 29, 30, 31, 34, 35, 36, 37]) total number of confs: 137 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901151/working/building/REAL300025569542 /scratch/stefan/7901151/working /scratch/stefan/7901151 Finished preparing REAL300025569542 Recording results /scratch/stefan/7901151/working /scratch/stefan/7901151 Appending to /scratch/stefan/7901151/finished/xaaaaat_worked.* 0: /scratch/stefan/7901151/working/building/REAL300025569542/0.* Removing working files in /scratch/stefan/7901151/working/building/REAL300025569542 Building REAL300025569543 mkdir: created directory `/scratch/stefan/7901151/working/building/REAL300025569543' /scratch/stefan/7901151/working/building/REAL300025569543 /scratch/stefan/7901151/working /scratch/stefan/7901151 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025569543 mkdir: created directory `0' /scratch/stefan/7901151/working/building/REAL300025569543/0 /scratch/stefan/7901151/working/building/REAL300025569543 /scratch/stefan/7901151/working /scratch/stefan/7901151 Protomer 0 (index: 41) Found valid previously generated 3D confromation in /scratch/stefan/7901151/working/3D/41 `/scratch/stefan/7901151/working/3D/41' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C1=CC(F)=CC(S(=O)(=O)NCC2=NC(=O)O[N-]2)=C1) `REAL300025569543.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025569543.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901151/working/building/REAL300025569543/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569543 none CCOC(=O)C1=CC(F)=CC(S(=O)(=O)NCC2=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', 'F', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 5, 12, 1, 11, 1, 1, 1, 15, 1, 1, 14, 11, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 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: [16, 8, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 27, 104, 104, 104, 104, 104, 1, 17, 17, 17, 16, 16, 1, 1, 9, 27, 27, 1] 201 rigid atoms, others: [33, 3, 5, 6, 7, 8, 9, 10, 11, 22, 28, 29] set([0, 1, 2, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 30, 31, 32]) 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: REAL300025569543 none CCOC(=O)C1=CC(F)=CC(S(=O)(=O)NCC2=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', 'F', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 5, 12, 1, 11, 1, 1, 1, 15, 1, 1, 14, 11, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 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, 191, 189, 104, 189, 104, 104, 104, 104, 104, 59, 44, 59, 59, 8, 1, 1, 1, 1, 1, 1, 1, 104, 201, 201, 201, 201, 201, 104, 104, 44, 8, 8, 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]) total number of confs: 629 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901151/working/building/REAL300025569543 /scratch/stefan/7901151/working /scratch/stefan/7901151 Finished preparing REAL300025569543 Recording results /scratch/stefan/7901151/working /scratch/stefan/7901151 Appending to /scratch/stefan/7901151/finished/xaaaaat_worked.* 0: /scratch/stefan/7901151/working/building/REAL300025569543/0.* Removing working files in /scratch/stefan/7901151/working/building/REAL300025569543 Building REAL300025569544 mkdir: created directory `/scratch/stefan/7901151/working/building/REAL300025569544' /scratch/stefan/7901151/working/building/REAL300025569544 /scratch/stefan/7901151/working /scratch/stefan/7901151 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025569544 mkdir: created directory `0' /scratch/stefan/7901151/working/building/REAL300025569544/0 /scratch/stefan/7901151/working/building/REAL300025569544 /scratch/stefan/7901151/working /scratch/stefan/7901151 Protomer 0 (index: 42) Found valid previously generated 3D confromation in /scratch/stefan/7901151/working/3D/42 `/scratch/stefan/7901151/working/3D/42' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CNS(=O)(=O)C2=CC=C3OCCCC3=C2)[N-]O1) `REAL300025569544.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025569544.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901151/working/building/REAL300025569544/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569544 none O=C1N=C(CNS(=O)(=O)C2=CC=C3OCCCC3=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', '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.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, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 5, 5, 1, 1, 8, 12, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 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, 9, 44, 77, 77, 77, 104, 104, 104, 104, 104, 104, 104, 104, 104, 1, 1, 9, 9, 44, 104, 104, 104, 104, 104, 104, 104, 104, 104] 104 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: 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: REAL300025569544 none O=C1N=C(CNS(=O)(=O)C2=CC=C3OCCCC3=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', '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.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, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 5, 5, 1, 1, 8, 12, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 104 conformations in input total number of sets (complete confs): 104 using faster count positions algorithm for large data unique positions, atoms: [104, 104, 104, 44, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 104, 104, 44, 44, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1] 104 rigid atoms, others: [32, 6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 8, 19, 20, 21, 22, 23]) total number of confs: 246 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901151/working/building/REAL300025569544 /scratch/stefan/7901151/working /scratch/stefan/7901151 Finished preparing REAL300025569544 Recording results /scratch/stefan/7901151/working /scratch/stefan/7901151 Appending to /scratch/stefan/7901151/finished/xaaaaat_worked.* 0: /scratch/stefan/7901151/working/building/REAL300025569544/0.* Removing working files in /scratch/stefan/7901151/working/building/REAL300025569544 Building REAL300025569545 mkdir: created directory `/scratch/stefan/7901151/working/building/REAL300025569545' /scratch/stefan/7901151/working/building/REAL300025569545 /scratch/stefan/7901151/working /scratch/stefan/7901151 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025569545 mkdir: created directory `0' /scratch/stefan/7901151/working/building/REAL300025569545/0 /scratch/stefan/7901151/working/building/REAL300025569545 /scratch/stefan/7901151/working /scratch/stefan/7901151 Protomer 0 (index: 43) Found valid previously generated 3D confromation in /scratch/stefan/7901151/working/3D/43 `/scratch/stefan/7901151/working/3D/43' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC(Cl)=CC=C1CS(=O)(=O)NCC1=NC(=O)O[N-]1) `REAL300025569545.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025569545.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901151/working/building/REAL300025569545/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569545 none N#CC1=CC(Cl)=CC=C1CS(=O)(=O)NCC1=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', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 5, 14, 11, 11, 8, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 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, 15, 15, 15, 43, 113, 201, 201, 201, 201, 201, 1, 1, 1, 4, 4, 43, 113, 113] 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: 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: REAL300025569545 none N#CC1=CC(Cl)=CC=C1CS(=O)(=O)NCC1=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', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 5, 14, 11, 11, 8, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 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, 163, 107, 58, 107, 107, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 163, 163, 58, 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: 762 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901151/working/building/REAL300025569545 /scratch/stefan/7901151/working /scratch/stefan/7901151 Finished preparing REAL300025569545 Recording results /scratch/stefan/7901151/working /scratch/stefan/7901151 Appending to /scratch/stefan/7901151/finished/xaaaaat_worked.* 0: /scratch/stefan/7901151/working/building/REAL300025569545/0.* Removing working files in /scratch/stefan/7901151/working/building/REAL300025569545 Building REAL300025569546 mkdir: created directory `/scratch/stefan/7901151/working/building/REAL300025569546' /scratch/stefan/7901151/working/building/REAL300025569546 /scratch/stefan/7901151/working /scratch/stefan/7901151 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025569546 mkdir: created directory `0' /scratch/stefan/7901151/working/building/REAL300025569546/0 /scratch/stefan/7901151/working/building/REAL300025569546 /scratch/stefan/7901151/working /scratch/stefan/7901151 Protomer 0 (index: 44) Found valid previously generated 3D confromation in /scratch/stefan/7901151/working/3D/44 `/scratch/stefan/7901151/working/3D/44' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CNS(=O)(=O)C2=CC=CC=C2CN2C=NC=N2)[N-]O1) `REAL300025569546.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025569546.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901151/working/building/REAL300025569546/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569546 none O=C1N=C(CNS(=O)(=O)C2=CC=CC=C2CN2C=NC=N2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 5, 8, 1, 8, 1, 8, 8, 12, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 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 88 conformations in input total number of sets (complete confs): 88 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 9, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 71, 88, 88, 88, 88, 1, 1, 9, 9, 35, 35, 35, 35, 35, 71, 71, 88, 88] 88 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: 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569546 none O=C1N=C(CNS(=O)(=O)C2=CC=CC=C2CN2C=NC=N2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 5, 8, 1, 8, 1, 8, 8, 12, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 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 88 conformations in input total number of sets (complete confs): 88 using faster count positions algorithm for large data unique positions, atoms: [88, 88, 88, 38, 19, 19, 17, 19, 19, 17, 17, 10, 17, 17, 9, 1, 1, 1, 1, 1, 1, 88, 88, 38, 38, 19, 17, 9, 17, 17, 9, 9, 1, 1] 88 rigid atoms, others: [32, 33, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 247 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569546 none O=C1N=C(CNS(=O)(=O)C2=CC=CC=C2CN2C=NC=N2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 5, 8, 1, 8, 1, 8, 8, 12, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 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 88 conformations in input total number of sets (complete confs): 88 using faster count positions algorithm for large data unique positions, atoms: [35, 35, 35, 7, 3, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 6, 17, 17, 17, 17, 35, 35, 7, 7, 3, 1, 1, 1, 1, 6, 6, 17, 17] 88 rigid atoms, others: [6, 9, 10, 11, 12, 13, 14, 15, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33]) total number of confs: 96 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901151/working/building/REAL300025569546 /scratch/stefan/7901151/working /scratch/stefan/7901151 Finished preparing REAL300025569546 Recording results /scratch/stefan/7901151/working /scratch/stefan/7901151 Appending to /scratch/stefan/7901151/finished/xaaaaat_worked.* 0: /scratch/stefan/7901151/working/building/REAL300025569546/0.* Removing working files in /scratch/stefan/7901151/working/building/REAL300025569546 Building REAL300025569547 mkdir: created directory `/scratch/stefan/7901151/working/building/REAL300025569547' /scratch/stefan/7901151/working/building/REAL300025569547 /scratch/stefan/7901151/working /scratch/stefan/7901151 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025569547 mkdir: created directory `0' /scratch/stefan/7901151/working/building/REAL300025569547/0 /scratch/stefan/7901151/working/building/REAL300025569547 /scratch/stefan/7901151/working /scratch/stefan/7901151 Protomer 0 (index: 45) Found valid previously generated 3D confromation in /scratch/stefan/7901151/working/3D/45 `/scratch/stefan/7901151/working/3D/45' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=C(S(=O)(=O)NCC2=NC(=O)O[N-]2)C=C(C(=O)OC)O1) `REAL300025569547.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025569547.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901151/working/building/REAL300025569547/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569547 none CCC1=C(S(=O)(=O)NCC2=NC(=O)O[N-]2)C=C(C(=O)OC)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 14, 11, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 11, 12, 5, 12, 7, 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, 5, 3, 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: [6, 1, 1, 1, 1, 5, 5, 5, 13, 43, 135, 135, 135, 135, 135, 1, 1, 1, 7, 7, 7, 1, 6, 6, 6, 6, 6, 13, 43, 43, 1, 7, 7, 7] 201 rigid atoms, others: [1, 2, 3, 4, 15, 16, 17, 21, 30] set([0, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33]) 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: REAL300025569547 none CCC1=C(S(=O)(=O)NCC2=NC(=O)O[N-]2)C=C(C(=O)OC)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 14, 11, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 11, 12, 5, 12, 7, 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, 5, 3, 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: [152, 135, 135, 90, 48, 90, 90, 8, 1, 1, 1, 1, 1, 1, 1, 135, 135, 135, 191, 191, 191, 135, 152, 152, 152, 152, 152, 48, 8, 8, 135, 191, 191, 191] 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: 739 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901151/working/building/REAL300025569547 /scratch/stefan/7901151/working /scratch/stefan/7901151 Finished preparing REAL300025569547 Recording results /scratch/stefan/7901151/working /scratch/stefan/7901151 Appending to /scratch/stefan/7901151/finished/xaaaaat_worked.* 0: /scratch/stefan/7901151/working/building/REAL300025569547/0.* Removing working files in /scratch/stefan/7901151/working/building/REAL300025569547 Building REAL300025569548 mkdir: created directory `/scratch/stefan/7901151/working/building/REAL300025569548' /scratch/stefan/7901151/working/building/REAL300025569548 /scratch/stefan/7901151/working /scratch/stefan/7901151 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025569548 mkdir: created directory `0' /scratch/stefan/7901151/working/building/REAL300025569548/0 /scratch/stefan/7901151/working/building/REAL300025569548 /scratch/stefan/7901151/working /scratch/stefan/7901151 Protomer 0 (index: 46) Found valid previously generated 3D confromation in /scratch/stefan/7901151/working/3D/46 `/scratch/stefan/7901151/working/3D/46' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)OC1=CC=C(S(=O)(=O)NCC2=NC(=O)O[N-]2)C=C1) `REAL300025569548.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025569548.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901151/working/building/REAL300025569548/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569548 none CC(C)OC1=CC=C(S(=O)(=O)NCC2=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.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 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, 5, 12, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 33, 139, 139, 139, 139, 139, 1, 1, 12, 12, 12, 12, 12, 12, 12, 1, 1, 9, 33, 33, 1, 1] 201 rigid atoms, others: [33, 34, 3, 4, 5, 6, 7, 8, 19, 20, 28, 29] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32]) total number of confs: 292 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: REAL300025569548 none CC(C)OC1=CC=C(S(=O)(=O)NCC2=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.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 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, 89, 89, 139, 139, 89, 49, 89, 89, 8, 1, 1, 1, 1, 1, 1, 1, 139, 139, 201, 201, 201, 201, 201, 201, 201, 139, 139, 49, 8, 8, 139, 139] 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: 763 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901151/working/building/REAL300025569548 /scratch/stefan/7901151/working /scratch/stefan/7901151 Finished preparing REAL300025569548 Recording results /scratch/stefan/7901151/working /scratch/stefan/7901151 Appending to /scratch/stefan/7901151/finished/xaaaaat_worked.* 0: /scratch/stefan/7901151/working/building/REAL300025569548/0.* Removing working files in /scratch/stefan/7901151/working/building/REAL300025569548 Building REAL300025569549 mkdir: created directory `/scratch/stefan/7901151/working/building/REAL300025569549' /scratch/stefan/7901151/working/building/REAL300025569549 /scratch/stefan/7901151/working /scratch/stefan/7901151 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025569549 mkdir: created directory `0' /scratch/stefan/7901151/working/building/REAL300025569549/0 /scratch/stefan/7901151/working/building/REAL300025569549 /scratch/stefan/7901151/working /scratch/stefan/7901151 Protomer 0 (index: 47) Found valid previously generated 3D confromation in /scratch/stefan/7901151/working/3D/47 `/scratch/stefan/7901151/working/3D/47' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCS(=O)(=O)NCCC1=CC=C(S(=O)(=O)NCC2=NC(=O)O[N-]2)S1) `REAL300025569549.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025569549.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901151/working/building/REAL300025569549/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569549 none CCS(=O)(=O)NCCC1=CC=C(S(=O)(=O)NCC2=NC(=O)O[N-]2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 11, 11, 8, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 8, 1, 11, 12, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 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: [33, 30, 27, 30, 30, 9, 4, 1, 1, 1, 1, 1, 1, 7, 7, 7, 20, 46, 118, 118, 118, 118, 118, 1, 33, 33, 33, 33, 33, 27, 9, 9, 4, 4, 1, 1, 20, 46, 46] 201 rigid atoms, others: [34, 35, 7, 8, 9, 10, 11, 12, 23] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38]) total number of confs: 409 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569549 none CCS(=O)(=O)NCCC1=CC=C(S(=O)(=O)NCC2=NC(=O)O[N-]2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 11, 11, 8, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 8, 1, 11, 12, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 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, 170, 126, 118, 118, 118, 118, 54, 36, 54, 54, 8, 1, 1, 1, 1, 1, 1, 1, 118, 201, 201, 201, 201, 201, 201, 170, 170, 126, 126, 118, 118, 36, 8, 8] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 710 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901151/working/building/REAL300025569549 /scratch/stefan/7901151/working /scratch/stefan/7901151 Finished preparing REAL300025569549 Recording results /scratch/stefan/7901151/working /scratch/stefan/7901151 Appending to /scratch/stefan/7901151/finished/xaaaaat_worked.* 0: /scratch/stefan/7901151/working/building/REAL300025569549/0.* Removing working files in /scratch/stefan/7901151/working/building/REAL300025569549 Building REAL300025569550 mkdir: created directory `/scratch/stefan/7901151/working/building/REAL300025569550' /scratch/stefan/7901151/working/building/REAL300025569550 /scratch/stefan/7901151/working /scratch/stefan/7901151 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025569550 mkdir: created directory `0' /scratch/stefan/7901151/working/building/REAL300025569550/0 /scratch/stefan/7901151/working/building/REAL300025569550 /scratch/stefan/7901151/working /scratch/stefan/7901151 Protomer 0 (index: 48) Found valid previously generated 3D confromation in /scratch/stefan/7901151/working/3D/48 `/scratch/stefan/7901151/working/3D/48' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(S(=O)(=O)NCC2=NC(=O)O[N-]2)C2=NC=CC=C2C=C1) `REAL300025569550.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025569550.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901151/working/building/REAL300025569550/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569550 none CC1=C(S(=O)(=O)NCC2=NC(=O)O[N-]2)C2=NC=CC=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.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 8, 1, 1, 1, 1, 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, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 66 conformations in input total number of sets (complete confs): 66 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 5, 5, 5, 9, 29, 66, 66, 66, 66, 66, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 29, 29, 1, 1, 1, 1, 1] 66 rigid atoms, others: [0, 1, 2, 3, 32, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27]) total number of confs: 180 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: REAL300025569550 none CC1=C(S(=O)(=O)NCC2=NC(=O)O[N-]2)C2=NC=CC=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.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 8, 1, 1, 1, 1, 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, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 66 conformations in input total number of sets (complete confs): 66 using faster count positions algorithm for large data unique positions, atoms: [66, 66, 64, 39, 64, 64, 8, 1, 1, 1, 1, 1, 1, 1, 66, 66, 66, 66, 66, 66, 66, 66, 66, 66, 66, 39, 8, 8, 66, 66, 66, 66, 66] 66 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 248 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901151/working/building/REAL300025569550 /scratch/stefan/7901151/working /scratch/stefan/7901151 Finished preparing REAL300025569550 Recording results /scratch/stefan/7901151/working /scratch/stefan/7901151 Appending to /scratch/stefan/7901151/finished/xaaaaat_worked.* 0: /scratch/stefan/7901151/working/building/REAL300025569550/0.* Removing working files in /scratch/stefan/7901151/working/building/REAL300025569550 Building REAL300025569551 mkdir: created directory `/scratch/stefan/7901151/working/building/REAL300025569551' /scratch/stefan/7901151/working/building/REAL300025569551 /scratch/stefan/7901151/working /scratch/stefan/7901151 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025569551 mkdir: created directory `0' /scratch/stefan/7901151/working/building/REAL300025569551/0 /scratch/stefan/7901151/working/building/REAL300025569551 /scratch/stefan/7901151/working /scratch/stefan/7901151 Protomer 0 (index: 49) Found valid previously generated 3D confromation in /scratch/stefan/7901151/working/3D/49 `/scratch/stefan/7901151/working/3D/49' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CNS(=O)(=O)C2=CC=CC=C2C2=CC=NO2)[N-]O1) `REAL300025569551.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025569551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901151/working/building/REAL300025569551/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569551 none O=C1N=C(CNS(=O)(=O)C2=CC=CC=C2C2=CC=NO2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'O.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 12, 8, 12, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 76 conformations in input total number of sets (complete confs): 76 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 9, 39, 57, 57, 57, 57, 57, 57, 57, 57, 57, 76, 76, 76, 76, 1, 1, 9, 9, 39, 57, 57, 57, 57, 76, 76] 76 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: 244 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569551 none O=C1N=C(CNS(=O)(=O)C2=CC=CC=C2C2=CC=NO2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'O.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 12, 8, 12, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 76 conformations in input total number of sets (complete confs): 76 using faster count positions algorithm for large data unique positions, atoms: [76, 76, 76, 33, 11, 7, 5, 7, 7, 5, 5, 4, 5, 5, 1, 1, 1, 1, 1, 1, 76, 76, 33, 33, 11, 5, 5, 5, 5, 1, 1] 76 rigid atoms, others: [14, 15, 16, 17, 18, 19, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 208 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569551 none O=C1N=C(CNS(=O)(=O)C2=CC=CC=C2C2=CC=NO2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'O.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 12, 8, 12, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 76 conformations in input total number of sets (complete confs): 76 using faster count positions algorithm for large data unique positions, atoms: [57, 57, 57, 17, 5, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 57, 57, 17, 17, 5, 1, 1, 1, 1, 5, 5] 76 rigid atoms, others: [6, 9, 10, 11, 12, 13, 14, 15, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30]) total number of confs: 125 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901151/working/building/REAL300025569551 /scratch/stefan/7901151/working /scratch/stefan/7901151 Finished preparing REAL300025569551 Recording results /scratch/stefan/7901151/working /scratch/stefan/7901151 Appending to /scratch/stefan/7901151/finished/xaaaaat_worked.* 0: /scratch/stefan/7901151/working/building/REAL300025569551/0.* Removing working files in /scratch/stefan/7901151/working/building/REAL300025569551 Building REAL300025569552 mkdir: created directory `/scratch/stefan/7901151/working/building/REAL300025569552' /scratch/stefan/7901151/working/building/REAL300025569552 /scratch/stefan/7901151/working /scratch/stefan/7901151 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025569552 mkdir: created directory `0' /scratch/stefan/7901151/working/building/REAL300025569552/0 /scratch/stefan/7901151/working/building/REAL300025569552 /scratch/stefan/7901151/working /scratch/stefan/7901151 Protomer 0 (index: 50) Found valid previously generated 3D confromation in /scratch/stefan/7901151/working/3D/50 `/scratch/stefan/7901151/working/3D/50' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC1=CC=C(S(=O)(=O)NCC2=NC(=O)O[N-]2)C2=CC=CC=C12) `REAL300025569552.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025569552.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901151/working/building/REAL300025569552/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569552 none CC(=O)NC1=CC=C(S(=O)(=O)NCC2=NC(=O)O[N-]2)C2=CC=CC=C12 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.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, 11, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 6, 7, 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, 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 98 conformations in input total number of sets (complete confs): 98 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 25, 62, 62, 62, 62, 62, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 1, 1, 5, 25, 25, 1, 1, 1, 1] 98 rigid atoms, others: [35, 34, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 36, 29, 30, 37] set([0, 1, 2, 33, 32, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 31]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569552 none CC(=O)NC1=CC=C(S(=O)(=O)NCC2=NC(=O)O[N-]2)C2=CC=CC=C12 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.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, 11, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 6, 7, 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, 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 98 conformations in input total number of sets (complete confs): 98 using faster count positions algorithm for large data unique positions, atoms: [98, 98, 98, 62, 62, 62, 62, 62, 48, 62, 62, 8, 1, 1, 1, 1, 1, 1, 1, 62, 62, 62, 62, 62, 62, 98, 98, 98, 98, 62, 62, 48, 8, 8, 62, 62, 62, 62] 98 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: 327 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901151/working/building/REAL300025569552 /scratch/stefan/7901151/working /scratch/stefan/7901151 Finished preparing REAL300025569552 Recording results /scratch/stefan/7901151/working /scratch/stefan/7901151 Appending to /scratch/stefan/7901151/finished/xaaaaat_worked.* 0: /scratch/stefan/7901151/working/building/REAL300025569552/0.* Removing working files in /scratch/stefan/7901151/working/building/REAL300025569552 Building REAL300025569553 mkdir: created directory `/scratch/stefan/7901151/working/building/REAL300025569553' /scratch/stefan/7901151/working/building/REAL300025569553 /scratch/stefan/7901151/working /scratch/stefan/7901151 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025569553 mkdir: created directory `0' /scratch/stefan/7901151/working/building/REAL300025569553/0 /scratch/stefan/7901151/working/building/REAL300025569553 /scratch/stefan/7901151/working /scratch/stefan/7901151 Protomer 0 (index: 51) Found valid previously generated 3D confromation in /scratch/stefan/7901151/working/3D/51 `/scratch/stefan/7901151/working/3D/51' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CNS(=O)(=O)CCCN2CCOCC2)[N-]O1) `REAL300025569553.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025569553.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901151/working/building/REAL300025569553/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569553 none O=C1N=C(CNS(=O)(=O)CCCN2CCOCC2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 8, 14, 11, 11, 5, 5, 5, 10, 5, 5, 12, 5, 5, 8, 12, 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, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in 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, 35, 47, 47, 47, 114, 128, 161, 201, 201, 201, 201, 201, 1, 1, 9, 9, 35, 114, 114, 128, 128, 161, 161, 201, 201, 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, 31, 32, 33, 34, 35, 36]) total number of confs: 812 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569553 none O=C1N=C(CNS(=O)(=O)CCCN2CCOCC2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 8, 14, 11, 11, 5, 5, 5, 10, 5, 5, 12, 5, 5, 8, 12, 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, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 126, 73, 32, 11, 32, 32, 5, 3, 1, 1, 1, 1, 1, 1, 1, 201, 201, 126, 126, 73, 11, 11, 5, 5, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 11, 12, 13, 14, 15, 16, 17, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 640 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901151/working/building/REAL300025569553 /scratch/stefan/7901151/working /scratch/stefan/7901151 Finished preparing REAL300025569553 Recording results /scratch/stefan/7901151/working /scratch/stefan/7901151 Appending to /scratch/stefan/7901151/finished/xaaaaat_worked.* 0: /scratch/stefan/7901151/working/building/REAL300025569553/0.* Removing working files in /scratch/stefan/7901151/working/building/REAL300025569553 Building REAL300025569554 mkdir: created directory `/scratch/stefan/7901151/working/building/REAL300025569554' /scratch/stefan/7901151/working/building/REAL300025569554 /scratch/stefan/7901151/working /scratch/stefan/7901151 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025569554 mkdir: created directory `0' /scratch/stefan/7901151/working/building/REAL300025569554/0 /scratch/stefan/7901151/working/building/REAL300025569554 /scratch/stefan/7901151/working /scratch/stefan/7901151 Protomer 0 (index: 52) Found valid previously generated 3D confromation in /scratch/stefan/7901151/working/3D/52 `/scratch/stefan/7901151/working/3D/52' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CNS(=O)(=O)C2=CC=C(OCC(F)(F)F)N=C2)[N-]O1) `REAL300025569554.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025569554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901151/working/building/REAL300025569554/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569554 none O=C1N=C(CNS(=O)(=O)C2=CC=C(OCC(F)(F)F)N=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', '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', 'F', 'N.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 5, 15, 15, 15, 8, 1, 8, 12, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 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, 43, 62, 62, 62, 110, 110, 110, 110, 140, 201, 201, 201, 201, 110, 110, 1, 1, 9, 9, 43, 110, 110, 201, 201, 110] 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: 731 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569554 none O=C1N=C(CNS(=O)(=O)C2=CC=C(OCC(F)(F)F)N=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', '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', 'F', 'N.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 5, 15, 15, 15, 8, 1, 8, 12, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 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: [110, 110, 110, 29, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 3, 14, 14, 14, 14, 1, 1, 110, 110, 29, 29, 9, 1, 1, 14, 14, 1] 201 rigid atoms, others: [6, 9, 10, 11, 12, 13, 19, 20, 26, 27, 30] set([0, 1, 2, 3, 4, 5, 7, 8, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 28, 29]) total number of confs: 257 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901151/working/building/REAL300025569554 /scratch/stefan/7901151/working /scratch/stefan/7901151 Finished preparing REAL300025569554 Recording results /scratch/stefan/7901151/working /scratch/stefan/7901151 Appending to /scratch/stefan/7901151/finished/xaaaaat_worked.* 0: /scratch/stefan/7901151/working/building/REAL300025569554/0.* Removing working files in /scratch/stefan/7901151/working/building/REAL300025569554 Building REAL300025569555 mkdir: created directory `/scratch/stefan/7901151/working/building/REAL300025569555' /scratch/stefan/7901151/working/building/REAL300025569555 /scratch/stefan/7901151/working /scratch/stefan/7901151 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025569555 mkdir: created directory `0' /scratch/stefan/7901151/working/building/REAL300025569555/0 /scratch/stefan/7901151/working/building/REAL300025569555 /scratch/stefan/7901151/working /scratch/stefan/7901151 Protomer 0 (index: 53) Found valid previously generated 3D confromation in /scratch/stefan/7901151/working/3D/53 `/scratch/stefan/7901151/working/3D/53' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(F)=CC=C1S(=O)(=O)NCC1=NC(=O)O[N-]1) `REAL300025569555.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025569555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901151/working/building/REAL300025569555/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569555 none COC(=O)C1=CC(F)=CC=C1S(=O)(=O)NCC1=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', 'F', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 1, 1, 15, 1, 1, 1, 14, 11, 11, 8, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 6, 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, 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, 1, 1, 5, 5, 5, 11, 47, 143, 143, 143, 143, 143, 11, 11, 11, 1, 1, 1, 11, 47, 47] 201 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 11, 25, 26, 27] set([0, 1, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30]) 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: REAL300025569555 none COC(=O)C1=CC(F)=CC=C1S(=O)(=O)NCC1=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', 'F', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 1, 1, 15, 1, 1, 1, 14, 11, 11, 8, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 6, 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, 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, 143, 201, 143, 143, 124, 143, 143, 143, 109, 57, 109, 109, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 143, 143, 143, 57, 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: 800 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901151/working/building/REAL300025569555 /scratch/stefan/7901151/working /scratch/stefan/7901151 Finished preparing REAL300025569555 Recording results /scratch/stefan/7901151/working /scratch/stefan/7901151 Appending to /scratch/stefan/7901151/finished/xaaaaat_worked.* 0: /scratch/stefan/7901151/working/building/REAL300025569555/0.* Removing working files in /scratch/stefan/7901151/working/building/REAL300025569555 Building REAL300025569556 mkdir: created directory `/scratch/stefan/7901151/working/building/REAL300025569556' /scratch/stefan/7901151/working/building/REAL300025569556 /scratch/stefan/7901151/working /scratch/stefan/7901151 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025569556 mkdir: created directory `0' /scratch/stefan/7901151/working/building/REAL300025569556/0 /scratch/stefan/7901151/working/building/REAL300025569556 /scratch/stefan/7901151/working /scratch/stefan/7901151 Protomer 0 (index: 54) Found valid previously generated 3D confromation in /scratch/stefan/7901151/working/3D/54 `/scratch/stefan/7901151/working/3D/54' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(Br)C(S(=O)(=O)NCC2=NC(=O)O[N-]2)=C1) `REAL300025569556.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025569556.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901151/working/building/REAL300025569556/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569556 none CC1=CC=C(Br)C(S(=O)(=O)NCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 17, 1, 14, 11, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 66 conformations in input total number of sets (complete confs): 66 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 9, 31, 66, 66, 66, 66, 66, 1, 2, 2, 2, 1, 1, 9, 31, 31, 1] 66 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 18, 22, 23, 27] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 24, 25, 26]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569556 none CC1=CC=C(Br)C(S(=O)(=O)NCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 17, 1, 14, 11, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 66 conformations in input total number of sets (complete confs): 66 using faster count positions algorithm for large data unique positions, atoms: [66, 66, 66, 66, 66, 66, 66, 47, 66, 66, 8, 1, 1, 1, 1, 1, 1, 1, 66, 66, 66, 66, 66, 66, 47, 8, 8, 66] 66 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: 224 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901151/working/building/REAL300025569556 /scratch/stefan/7901151/working /scratch/stefan/7901151 Finished preparing REAL300025569556 Recording results /scratch/stefan/7901151/working /scratch/stefan/7901151 Appending to /scratch/stefan/7901151/finished/xaaaaat_worked.* 0: /scratch/stefan/7901151/working/building/REAL300025569556/0.* Removing working files in /scratch/stefan/7901151/working/building/REAL300025569556 Building REAL300025569557 mkdir: created directory `/scratch/stefan/7901151/working/building/REAL300025569557' /scratch/stefan/7901151/working/building/REAL300025569557 /scratch/stefan/7901151/working /scratch/stefan/7901151 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025569557 mkdir: created directory `0' /scratch/stefan/7901151/working/building/REAL300025569557/0 /scratch/stefan/7901151/working/building/REAL300025569557 /scratch/stefan/7901151/working /scratch/stefan/7901151 Protomer 0 (index: 55) Found valid previously generated 3D confromation in /scratch/stefan/7901151/working/3D/55 `/scratch/stefan/7901151/working/3D/55' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(Cl)C(S(=O)(=O)NCC2=NC(=O)O[N-]2)=C1) `REAL300025569557.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025569557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901151/working/building/REAL300025569557/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569557 none CC1=CC=C(Cl)C(S(=O)(=O)NCC2=NC(=O)O[N-]2)=C1 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.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 16, 1, 14, 11, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 93 conformations in input total number of sets (complete confs): 93 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 13, 43, 93, 93, 93, 93, 93, 1, 2, 2, 2, 1, 1, 13, 43, 43, 1] 93 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 18, 22, 23, 27] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 24, 25, 26]) total number of confs: 252 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569557 none CC1=CC=C(Cl)C(S(=O)(=O)NCC2=NC(=O)O[N-]2)=C1 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.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 16, 1, 14, 11, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 93 conformations in input total number of sets (complete confs): 93 using faster count positions algorithm for large data unique positions, atoms: [93, 93, 93, 93, 93, 93, 77, 51, 77, 77, 8, 1, 1, 1, 1, 1, 1, 1, 93, 93, 93, 93, 93, 93, 51, 8, 8, 93] 93 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: 291 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901151/working/building/REAL300025569557 /scratch/stefan/7901151/working /scratch/stefan/7901151 Finished preparing REAL300025569557 Recording results /scratch/stefan/7901151/working /scratch/stefan/7901151 Appending to /scratch/stefan/7901151/finished/xaaaaat_worked.* 0: /scratch/stefan/7901151/working/building/REAL300025569557/0.* Removing working files in /scratch/stefan/7901151/working/building/REAL300025569557 Building REAL300025569558 mkdir: created directory `/scratch/stefan/7901151/working/building/REAL300025569558' /scratch/stefan/7901151/working/building/REAL300025569558 /scratch/stefan/7901151/working /scratch/stefan/7901151 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025569558 mkdir: created directory `0' /scratch/stefan/7901151/working/building/REAL300025569558/0 /scratch/stefan/7901151/working/building/REAL300025569558 /scratch/stefan/7901151/working /scratch/stefan/7901151 Protomer 0 (index: 56) Found valid previously generated 3D confromation in /scratch/stefan/7901151/working/3D/56 `/scratch/stefan/7901151/working/3D/56' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CNS(=O)(=O)CC2=CC=C(F)C=C2F)[N-]O1) `REAL300025569558.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025569558.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901151/working/building/REAL300025569558/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569558 none O=C1N=C(CNS(=O)(=O)CC2=CC=C(F)C=C2F)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', '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', 'F', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 8, 14, 11, 11, 5, 1, 1, 1, 1, 15, 1, 1, 15, 8, 12, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [5, 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] 0 hydrogens need rotated 201 conformations in 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, 53, 93, 93, 93, 165, 201, 201, 201, 201, 201, 201, 201, 1, 1, 9, 9, 53, 165, 165, 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: 799 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569558 none O=C1N=C(CNS(=O)(=O)CC2=CC=C(F)C=C2F)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', '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', 'F', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 8, 14, 11, 11, 5, 1, 1, 1, 1, 15, 1, 1, 15, 8, 12, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [5, 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] 0 hydrogens need rotated 201 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, 57, 24, 6, 24, 24, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 116, 116, 57, 6, 6, 1, 1, 1] 201 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 586 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901151/working/building/REAL300025569558 /scratch/stefan/7901151/working /scratch/stefan/7901151 Finished preparing REAL300025569558 Recording results /scratch/stefan/7901151/working /scratch/stefan/7901151 Appending to /scratch/stefan/7901151/finished/xaaaaat_worked.* 0: /scratch/stefan/7901151/working/building/REAL300025569558/0.* Removing working files in /scratch/stefan/7901151/working/building/REAL300025569558 Building REAL300025569559 mkdir: created directory `/scratch/stefan/7901151/working/building/REAL300025569559' /scratch/stefan/7901151/working/building/REAL300025569559 /scratch/stefan/7901151/working /scratch/stefan/7901151 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025569559 mkdir: created directory `0' /scratch/stefan/7901151/working/building/REAL300025569559/0 /scratch/stefan/7901151/working/building/REAL300025569559 /scratch/stefan/7901151/working /scratch/stefan/7901151 Protomer 0 (index: 57) Found valid previously generated 3D confromation in /scratch/stefan/7901151/working/3D/57 `/scratch/stefan/7901151/working/3D/57' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCS(=O)(=O)NC1=CC=C(S(=O)(=O)NCC2=NC(=O)O[N-]2)C=C1F) `REAL300025569559.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025569559.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901151/working/building/REAL300025569559/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569559 none CCS(=O)(=O)NC1=CC=C(S(=O)(=O)NCC2=NC(=O)O[N-]2)C=C1F NO_LONG_NAME dock atom types: ['C.3', '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.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, 5, 14, 11, 11, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 6, 4, 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 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [15, 12, 6, 12, 12, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 15, 15, 15, 15, 15, 1, 1, 1, 15, 15, 15, 15, 15, 6, 1, 1, 5, 5, 5, 1] 26 rigid atoms, others: [35, 5, 6, 7, 8, 9, 10, 21, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 32, 33, 34]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569559 none CCS(=O)(=O)NC1=CC=C(S(=O)(=O)NCC2=NC(=O)O[N-]2)C=C1F NO_LONG_NAME dock atom types: ['C.3', '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.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, 5, 14, 11, 11, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 6, 4, 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 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 23, 26, 26, 15, 15, 15, 15, 8, 8, 8, 8, 6, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 26, 26, 26, 26, 26, 23, 15, 15, 8, 6, 6, 15] 26 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: 87 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901151/working/building/REAL300025569559 /scratch/stefan/7901151/working /scratch/stefan/7901151 Finished preparing REAL300025569559 Recording results /scratch/stefan/7901151/working /scratch/stefan/7901151 Appending to /scratch/stefan/7901151/finished/xaaaaat_worked.* 0: /scratch/stefan/7901151/working/building/REAL300025569559/0.* Removing working files in /scratch/stefan/7901151/working/building/REAL300025569559 Building REAL300025569560 mkdir: created directory `/scratch/stefan/7901151/working/building/REAL300025569560' /scratch/stefan/7901151/working/building/REAL300025569560 /scratch/stefan/7901151/working /scratch/stefan/7901151 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025569560 mkdir: created directory `0' /scratch/stefan/7901151/working/building/REAL300025569560/0 /scratch/stefan/7901151/working/building/REAL300025569560 /scratch/stefan/7901151/working /scratch/stefan/7901151 Protomer 0 (index: 58) Found valid previously generated 3D confromation in /scratch/stefan/7901151/working/3D/58 `/scratch/stefan/7901151/working/3D/58' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(S(=O)(=O)NCC2=NC(=O)O[N-]2)=C(C)O1) `REAL300025569560.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025569560.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901151/working/building/REAL300025569560/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569560 none COC(=O)C1=CC(S(=O)(=O)NCC2=NC(=O)O[N-]2)=C(C)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.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 14, 11, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 5, 12, 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, 5, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 10, 1, 10, 1, 1, 1, 1, 5, 5, 5, 13, 49, 144, 144, 144, 144, 144, 1, 1, 1, 11, 10, 10, 1, 13, 49, 49, 2, 2, 2] 201 rigid atoms, others: [2, 4, 5, 6, 7, 18, 19, 20, 24] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 25, 26, 27, 28, 29, 30]) total number of confs: 348 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569560 none COC(=O)C1=CC(S(=O)(=O)NCC2=NC(=O)O[N-]2)=C(C)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.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 14, 11, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 5, 12, 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, 5, 3, 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, 144, 201, 144, 144, 110, 51, 110, 110, 8, 1, 1, 1, 1, 1, 1, 1, 144, 144, 144, 201, 201, 201, 144, 51, 8, 8, 144, 144, 144] 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: 722 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901151/working/building/REAL300025569560 /scratch/stefan/7901151/working /scratch/stefan/7901151 Finished preparing REAL300025569560 Recording results /scratch/stefan/7901151/working /scratch/stefan/7901151 Appending to /scratch/stefan/7901151/finished/xaaaaat_worked.* 0: /scratch/stefan/7901151/working/building/REAL300025569560/0.* Removing working files in /scratch/stefan/7901151/working/building/REAL300025569560 Building REAL300025569561 mkdir: created directory `/scratch/stefan/7901151/working/building/REAL300025569561' /scratch/stefan/7901151/working/building/REAL300025569561 /scratch/stefan/7901151/working /scratch/stefan/7901151 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025569561 mkdir: created directory `0' /scratch/stefan/7901151/working/building/REAL300025569561/0 /scratch/stefan/7901151/working/building/REAL300025569561 /scratch/stefan/7901151/working /scratch/stefan/7901151 Protomer 0 (index: 59) Found valid previously generated 3D confromation in /scratch/stefan/7901151/working/3D/59 `/scratch/stefan/7901151/working/3D/59' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(C1=CC=C(S(=O)(=O)NCC2=NC(=O)O[N-]2)C=C1F)N1CCCC1) `REAL300025569561.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025569561.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901151/working/building/REAL300025569561/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569561 none O=C(C1=CC=C(S(=O)(=O)NCC2=NC(=O)O[N-]2)C=C1F)N1CCCC1 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.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'F', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 15, 8, 5, 5, 5, 5, 7, 7, 6, 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, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 27, 129, 129, 129, 129, 129, 1, 1, 1, 7, 14, 14, 14, 14, 1, 1, 9, 27, 27, 1, 14, 14, 14, 14, 14, 14, 14, 14] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 17, 18, 19, 25, 26, 30] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 254 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569561 none O=C(C1=CC=C(S(=O)(=O)NCC2=NC(=O)O[N-]2)C=C1F)N1CCCC1 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.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'F', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 15, 8, 5, 5, 5, 5, 7, 7, 6, 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, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 14, 14, 6, 14, 22, 22, 22, 52, 113, 201, 201, 201, 201, 201, 14, 14, 14, 1, 1, 1, 1, 1, 14, 14, 52, 113, 113, 14, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 1, 34, 35, 36, 37, 38, 33, 20, 21, 22, 23, 24, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30]) total number of confs: 614 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569561 none O=C(C1=CC=C(S(=O)(=O)NCC2=NC(=O)O[N-]2)C=C1F)N1CCCC1 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.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'F', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 15, 8, 5, 5, 5, 5, 7, 7, 6, 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, 5, 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, 129, 129, 129, 129, 77, 41, 77, 77, 8, 1, 1, 1, 1, 1, 1, 1, 129, 129, 129, 201, 201, 201, 201, 201, 129, 129, 41, 8, 8, 129, 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]) total number of confs: 668 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901151/working/building/REAL300025569561 /scratch/stefan/7901151/working /scratch/stefan/7901151 Finished preparing REAL300025569561 Recording results /scratch/stefan/7901151/working /scratch/stefan/7901151 Appending to /scratch/stefan/7901151/finished/xaaaaat_worked.* 0: /scratch/stefan/7901151/working/building/REAL300025569561/0.* Removing working files in /scratch/stefan/7901151/working/building/REAL300025569561 Building REAL300025569562 mkdir: created directory `/scratch/stefan/7901151/working/building/REAL300025569562' /scratch/stefan/7901151/working/building/REAL300025569562 /scratch/stefan/7901151/working /scratch/stefan/7901151 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025569562 mkdir: created directory `0' /scratch/stefan/7901151/working/building/REAL300025569562/0 /scratch/stefan/7901151/working/building/REAL300025569562 /scratch/stefan/7901151/working /scratch/stefan/7901151 Protomer 0 (index: 60) Found valid previously generated 3D confromation in /scratch/stefan/7901151/working/3D/60 `/scratch/stefan/7901151/working/3D/60' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CNS(=O)(=O)C2=CN=C3NC=CC(Cl)=C23)[N-]O1) `REAL300025569562.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025569562.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901151/working/building/REAL300025569562/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569562 none O=C1N=C(CNS(=O)(=O)C2=CN=C3NC=CC(Cl)=C23)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', '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', 'Cl', 'C.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 8, 14, 11, 11, 1, 1, 8, 1, 8, 1, 1, 1, 16, 1, 8, 12, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 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: [1, 1, 1, 1, 1, 9, 39, 57, 57, 57, 57, 57, 57, 57, 57, 57, 57, 57, 57, 1, 1, 9, 9, 39, 57, 57, 57, 57] 57 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: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569562 none O=C1N=C(CNS(=O)(=O)C2=CN=C3NC=CC(Cl)=C23)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', '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', 'Cl', 'C.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 8, 14, 11, 11, 1, 1, 8, 1, 8, 1, 1, 1, 16, 1, 8, 12, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [57, 57, 57, 21, 5, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 57, 57, 21, 21, 5, 1, 1, 1, 1] 57 rigid atoms, others: [6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 7, 8, 19, 20, 21, 22, 23]) total number of confs: 132 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901151/working/building/REAL300025569562 /scratch/stefan/7901151/working /scratch/stefan/7901151 Finished preparing REAL300025569562 Recording results /scratch/stefan/7901151/working /scratch/stefan/7901151 Appending to /scratch/stefan/7901151/finished/xaaaaat_worked.* 0: /scratch/stefan/7901151/working/building/REAL300025569562/0.* Removing working files in /scratch/stefan/7901151/working/building/REAL300025569562 Building REAL300025569563 mkdir: created directory `/scratch/stefan/7901151/working/building/REAL300025569563' /scratch/stefan/7901151/working/building/REAL300025569563 /scratch/stefan/7901151/working /scratch/stefan/7901151 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025569563 mkdir: created directory `0' /scratch/stefan/7901151/working/building/REAL300025569563/0 /scratch/stefan/7901151/working/building/REAL300025569563 /scratch/stefan/7901151/working /scratch/stefan/7901151 Protomer 0 (index: 61) Found valid previously generated 3D confromation in /scratch/stefan/7901151/working/3D/61 `/scratch/stefan/7901151/working/3D/61' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CNS(=O)(=O)N2CCC3(CC2)OCCO3)[N-]O1) `REAL300025569563.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025569563.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901151/working/building/REAL300025569563/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569563 none O=C1N=C(CNS(=O)(=O)N2CCC3(CC2)OCCO3)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 8, 14, 11, 11, 8, 5, 5, 5, 5, 5, 12, 5, 5, 12, 8, 12, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 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, 7, 7, 7] 0 hydrogens need rotated 180 conformations in input total number of sets (complete confs): 180 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 9, 48, 138, 138, 138, 180, 180, 180, 180, 180, 180, 180, 180, 180, 1, 1, 9, 9, 48, 180, 180, 180, 180, 180, 180, 180, 180, 180, 180, 180, 180] 180 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, 35]) 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: REAL300025569563 none O=C1N=C(CNS(=O)(=O)N2CCC3(CC2)OCCO3)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 8, 14, 11, 11, 8, 5, 5, 5, 5, 5, 12, 5, 5, 12, 8, 12, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 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, 7, 7, 7] 0 hydrogens need rotated 180 conformations in input total number of sets (complete confs): 180 using faster count positions algorithm for large data unique positions, atoms: [180, 180, 180, 92, 22, 6, 1, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 180, 180, 92, 92, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 180 rigid atoms, others: [6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35] set([0, 1, 2, 3, 4, 5, 7, 8, 19, 20, 21, 22, 23]) total number of confs: 473 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901151/working/building/REAL300025569563 /scratch/stefan/7901151/working /scratch/stefan/7901151 Finished preparing REAL300025569563 Recording results /scratch/stefan/7901151/working /scratch/stefan/7901151 Appending to /scratch/stefan/7901151/finished/xaaaaat_worked.* 0: /scratch/stefan/7901151/working/building/REAL300025569563/0.* Removing working files in /scratch/stefan/7901151/working/building/REAL300025569563 Building REAL300025569564 mkdir: created directory `/scratch/stefan/7901151/working/building/REAL300025569564' /scratch/stefan/7901151/working/building/REAL300025569564 /scratch/stefan/7901151/working /scratch/stefan/7901151 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025569564 mkdir: created directory `0' /scratch/stefan/7901151/working/building/REAL300025569564/0 /scratch/stefan/7901151/working/building/REAL300025569564 /scratch/stefan/7901151/working /scratch/stefan/7901151 Protomer 0 (index: 62) Found valid previously generated 3D confromation in /scratch/stefan/7901151/working/3D/62 `/scratch/stefan/7901151/working/3D/62' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CNS(=O)(=O)C2=C(Cl)C=C(F)C=C2Br)[N-]O1) `REAL300025569564.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025569564.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901151/working/building/REAL300025569564/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569564 none O=C1N=C(CNS(=O)(=O)C2=C(Cl)C=C(F)C=C2Br)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 8, 14, 11, 11, 1, 1, 16, 1, 1, 15, 1, 1, 17, 8, 12, 7, 7, 6, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7] 0 hydrogens need rotated 145 conformations in input total number of sets (complete confs): 145 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 9, 57, 110, 110, 110, 145, 145, 145, 145, 145, 145, 145, 145, 1, 1, 9, 9, 57, 145, 145] 145 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]) 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: REAL300025569564 none O=C1N=C(CNS(=O)(=O)C2=C(Cl)C=C(F)C=C2Br)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 8, 14, 11, 11, 1, 1, 16, 1, 1, 15, 1, 1, 17, 8, 12, 7, 7, 6, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7] 0 hydrogens need rotated 145 conformations in input total number of sets (complete confs): 145 using faster count positions algorithm for large data unique positions, atoms: [145, 145, 145, 71, 21, 10, 1, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 145, 145, 71, 71, 21, 1, 1] 145 rigid atoms, others: [6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24] set([0, 1, 2, 3, 4, 5, 7, 8, 18, 19, 20, 21, 22]) total number of confs: 381 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901151/working/building/REAL300025569564 /scratch/stefan/7901151/working /scratch/stefan/7901151 mkdir: created directory `1' /scratch/stefan/7901151/working/building/REAL300025569564/1 /scratch/stefan/7901151/working/building/REAL300025569564 /scratch/stefan/7901151/working /scratch/stefan/7901151 Protomer 1 (index: 63) Found valid previously generated 3D confromation in /scratch/stefan/7901151/working/3D/63 `/scratch/stefan/7901151/working/3D/63' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(C[N-]S(=O)(=O)C2=C(Cl)C=C(F)C=C2Br)[N-]O1) `REAL300025569564.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025569564.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901151/working/building/REAL300025569564/1/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: REAL300025569564 none O=C1N=C(C[N-]S(=O)(=O)C2=C(Cl)C=C(F)C=C2Br)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'N.2', 'O.3', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 8, 14, 11, 11, 1, 1, 16, 1, 1, 15, 1, 1, 17, 8, 12, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7] 0 hydrogens need rotated 101 conformations in input total number of sets (complete confs): 101 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 9, 34, 74, 74, 74, 101, 101, 101, 74, 83, 101, 101, 101, 1, 1, 9, 9, 101, 101] 101 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]) 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: REAL300025569564 none O=C1N=C(C[N-]S(=O)(=O)C2=C(Cl)C=C(F)C=C2Br)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'N.2', 'O.3', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 8, 14, 11, 11, 1, 1, 16, 1, 1, 15, 1, 1, 17, 8, 12, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7] 0 hydrogens need rotated 101 conformations in input total number of sets (complete confs): 101 using faster count positions algorithm for large data unique positions, atoms: [101, 101, 101, 61, 21, 11, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 101, 101, 61, 61, 1, 1] 101 rigid atoms, others: [6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23] set([0, 1, 2, 3, 4, 5, 7, 8, 18, 19, 20, 21]) total number of confs: 296 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901151/working/building/REAL300025569564 /scratch/stefan/7901151/working /scratch/stefan/7901151 Finished preparing REAL300025569564 Recording results /scratch/stefan/7901151/working /scratch/stefan/7901151 Appending to /scratch/stefan/7901151/finished/xaaaaat_worked.* 0: /scratch/stefan/7901151/working/building/REAL300025569564/0.* 1: /scratch/stefan/7901151/working/building/REAL300025569564/1.* Removing working files in /scratch/stefan/7901151/working/building/REAL300025569564 Building REAL300025569565 mkdir: created directory `/scratch/stefan/7901151/working/building/REAL300025569565' /scratch/stefan/7901151/working/building/REAL300025569565 /scratch/stefan/7901151/working /scratch/stefan/7901151 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025569565 mkdir: created directory `0' /scratch/stefan/7901151/working/building/REAL300025569565/0 /scratch/stefan/7901151/working/building/REAL300025569565 /scratch/stefan/7901151/working /scratch/stefan/7901151 Protomer 0 (index: 64) Found valid previously generated 3D confromation in /scratch/stefan/7901151/working/3D/64 `/scratch/stefan/7901151/working/3D/64' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CNS(=O)(=O)C2=CN=C(Cl)C=C2Cl)[N-]O1) `REAL300025569565.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025569565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901151/working/building/REAL300025569565/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569565 none O=C1N=C(CNS(=O)(=O)C2=CN=C(Cl)C=C2Cl)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 8, 14, 11, 11, 1, 1, 8, 1, 16, 1, 1, 16, 8, 12, 7, 7, 6, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7] 0 hydrogens need rotated 82 conformations in input total number of sets (complete confs): 82 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 9, 50, 76, 76, 76, 82, 82, 82, 82, 82, 82, 82, 1, 1, 9, 9, 50, 82, 82] 82 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]) total number of confs: 282 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569565 none O=C1N=C(CNS(=O)(=O)C2=CN=C(Cl)C=C2Cl)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 8, 14, 11, 11, 1, 1, 8, 1, 16, 1, 1, 16, 8, 12, 7, 7, 6, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7] 0 hydrogens need rotated 82 conformations in input total number of sets (complete confs): 82 using faster count positions algorithm for large data unique positions, atoms: [82, 82, 82, 37, 11, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 82, 82, 37, 37, 11, 1, 1] 82 rigid atoms, others: [6, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23] set([0, 1, 2, 3, 4, 5, 7, 8, 17, 18, 19, 20, 21]) total number of confs: 210 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901151/working/building/REAL300025569565 /scratch/stefan/7901151/working /scratch/stefan/7901151 mkdir: created directory `1' /scratch/stefan/7901151/working/building/REAL300025569565/1 /scratch/stefan/7901151/working/building/REAL300025569565 /scratch/stefan/7901151/working /scratch/stefan/7901151 Protomer 1 (index: 65) Found valid previously generated 3D confromation in /scratch/stefan/7901151/working/3D/65 `/scratch/stefan/7901151/working/3D/65' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(C[N-]S(=O)(=O)C2=CN=C(Cl)C=C2Cl)[N-]O1) `REAL300025569565.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025569565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901151/working/building/REAL300025569565/1/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: REAL300025569565 none O=C1N=C(C[N-]S(=O)(=O)C2=CN=C(Cl)C=C2Cl)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'N.2', 'O.3', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 8, 14, 11, 11, 1, 1, 8, 1, 16, 1, 1, 16, 8, 12, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 9, 27, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 1, 1, 9, 9, 49, 49] 49 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]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569565 none O=C1N=C(C[N-]S(=O)(=O)C2=CN=C(Cl)C=C2Cl)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'N.2', 'O.3', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 8, 14, 11, 11, 1, 1, 8, 1, 16, 1, 1, 16, 8, 12, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 49, 31, 13, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 49, 49, 31, 31, 1, 1] 49 rigid atoms, others: [6, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22] set([0, 1, 2, 3, 4, 5, 7, 8, 17, 18, 19, 20]) total number of confs: 144 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901151/working/building/REAL300025569565 /scratch/stefan/7901151/working /scratch/stefan/7901151 Finished preparing REAL300025569565 Recording results /scratch/stefan/7901151/working /scratch/stefan/7901151 Appending to /scratch/stefan/7901151/finished/xaaaaat_worked.* 0: /scratch/stefan/7901151/working/building/REAL300025569565/0.* 1: /scratch/stefan/7901151/working/building/REAL300025569565/1.* Removing working files in /scratch/stefan/7901151/working/building/REAL300025569565 Building REAL300025569566 mkdir: created directory `/scratch/stefan/7901151/working/building/REAL300025569566' /scratch/stefan/7901151/working/building/REAL300025569566 /scratch/stefan/7901151/working /scratch/stefan/7901151 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025569566 mkdir: created directory `0' /scratch/stefan/7901151/working/building/REAL300025569566/0 /scratch/stefan/7901151/working/building/REAL300025569566 /scratch/stefan/7901151/working /scratch/stefan/7901151 Protomer 0 (index: 66) Found valid previously generated 3D confromation in /scratch/stefan/7901151/working/3D/66 `/scratch/stefan/7901151/working/3D/66' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCS(=O)(=O)NC1=CC=C(S(=O)(=O)NCC2=NC(=O)O[N-]2)C=C1F) `REAL300025569566.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025569566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901151/working/building/REAL300025569566/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569566 none CCCS(=O)(=O)NC1=CC=C(S(=O)(=O)NCC2=NC(=O)O[N-]2)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', '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.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 14, 11, 11, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 6, 4, 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 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [34, 32, 14, 7, 14, 14, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 17, 17, 17, 17, 17, 1, 1, 1, 34, 34, 34, 34, 34, 32, 32, 7, 1, 1, 5, 5, 5, 1] 57 rigid atoms, others: [33, 34, 38, 6, 7, 8, 9, 10, 11, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569566 none CCCS(=O)(=O)NC1=CC=C(S(=O)(=O)NCC2=NC(=O)O[N-]2)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', '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.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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 14, 11, 11, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 6, 4, 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 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [57, 57, 45, 31, 45, 45, 17, 17, 17, 17, 9, 9, 9, 9, 6, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 57, 57, 57, 57, 57, 57, 57, 31, 17, 17, 9, 6, 6, 17] 57 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: 240 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901151/working/building/REAL300025569566 /scratch/stefan/7901151/working /scratch/stefan/7901151 Finished preparing REAL300025569566 Recording results /scratch/stefan/7901151/working /scratch/stefan/7901151 Appending to /scratch/stefan/7901151/finished/xaaaaat_worked.* 0: /scratch/stefan/7901151/working/building/REAL300025569566/0.* Removing working files in /scratch/stefan/7901151/working/building/REAL300025569566 Building REAL300025569567 mkdir: created directory `/scratch/stefan/7901151/working/building/REAL300025569567' /scratch/stefan/7901151/working/building/REAL300025569567 /scratch/stefan/7901151/working /scratch/stefan/7901151 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025569567 mkdir: created directory `0' /scratch/stefan/7901151/working/building/REAL300025569567/0 /scratch/stefan/7901151/working/building/REAL300025569567 /scratch/stefan/7901151/working /scratch/stefan/7901151 Protomer 0 (index: 67) Found valid previously generated 3D confromation in /scratch/stefan/7901151/working/3D/67 `/scratch/stefan/7901151/working/3D/67' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C([N+](=O)[O-])C=C(S(=O)(=O)NCC2=NC(=O)O[N-]2)S1) `REAL300025569567.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025569567.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901151/working/building/REAL300025569567/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569567 none CC1=C([N+](=O)[O-])C=C(S(=O)(=O)NCC2=NC(=O)O[N-]2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 11, 11, 1, 1, 14, 11, 11, 8, 5, 1, 8, 1, 11, 12, 8, 14, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 172 conformations in input total number of sets (complete confs): 172 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 2, 1, 1, 1, 6, 6, 6, 25, 86, 172, 172, 172, 172, 172, 1, 2, 2, 2, 1, 25, 86, 86] 172 rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 19, 23] set([4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 24, 25, 26]) total number of confs: 455 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569567 none CC1=C([N+](=O)[O-])C=C(S(=O)(=O)NCC2=NC(=O)O[N-]2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 11, 11, 1, 1, 14, 11, 11, 8, 5, 1, 8, 1, 11, 12, 8, 14, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 172 conformations in input total number of sets (complete confs): 172 using faster count positions algorithm for large data unique positions, atoms: [172, 172, 172, 172, 172, 172, 172, 108, 55, 108, 108, 8, 1, 1, 1, 1, 1, 1, 1, 172, 172, 172, 172, 172, 55, 8, 8] 172 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]) total number of confs: 516 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901151/working/building/REAL300025569567 /scratch/stefan/7901151/working /scratch/stefan/7901151 Finished preparing REAL300025569567 Recording results /scratch/stefan/7901151/working /scratch/stefan/7901151 Appending to /scratch/stefan/7901151/finished/xaaaaat_worked.* 0: /scratch/stefan/7901151/working/building/REAL300025569567/0.* Removing working files in /scratch/stefan/7901151/working/building/REAL300025569567 Building REAL300025569568 mkdir: created directory `/scratch/stefan/7901151/working/building/REAL300025569568' /scratch/stefan/7901151/working/building/REAL300025569568 /scratch/stefan/7901151/working /scratch/stefan/7901151 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025569568 mkdir: created directory `0' /scratch/stefan/7901151/working/building/REAL300025569568/0 /scratch/stefan/7901151/working/building/REAL300025569568 /scratch/stefan/7901151/working /scratch/stefan/7901151 Protomer 0 (index: 68) Found valid previously generated 3D confromation in /scratch/stefan/7901151/working/3D/68 `/scratch/stefan/7901151/working/3D/68' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)S(=O)(=O)CCCS(=O)(=O)NCC1=NC(=O)O[N-]1) `REAL300025569568.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025569568.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901151/working/building/REAL300025569568/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569568 none CN(C)S(=O)(=O)CCCS(=O)(=O)NCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', '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.2', 'N.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, 8, 5, 14, 11, 11, 5, 5, 5, 14, 11, 11, 8, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 6, 4, 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 4 conformations in input total number of sets (complete confs): 4 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] 4 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: 13 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901151/working/building/REAL300025569568 /scratch/stefan/7901151/working /scratch/stefan/7901151 Finished preparing REAL300025569568 Recording results /scratch/stefan/7901151/working /scratch/stefan/7901151 Appending to /scratch/stefan/7901151/finished/xaaaaat_worked.* 0: /scratch/stefan/7901151/working/building/REAL300025569568/0.* Removing working files in /scratch/stefan/7901151/working/building/REAL300025569568 Building REAL300025569569 mkdir: created directory `/scratch/stefan/7901151/working/building/REAL300025569569' /scratch/stefan/7901151/working/building/REAL300025569569 /scratch/stefan/7901151/working /scratch/stefan/7901151 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025569569 mkdir: created directory `0' /scratch/stefan/7901151/working/building/REAL300025569569/0 /scratch/stefan/7901151/working/building/REAL300025569569 /scratch/stefan/7901151/working /scratch/stefan/7901151 Protomer 0 (index: 69) Found valid previously generated 3D confromation in /scratch/stefan/7901151/working/3D/69 `/scratch/stefan/7901151/working/3D/69' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(S(=O)(=O)NCC2=NC(=O)O[N-]2)=CN=C1Cl) `REAL300025569569.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025569569.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901151/working/building/REAL300025569569/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569569 none COC1=CC(S(=O)(=O)NCC2=NC(=O)O[N-]2)=CN=C1Cl 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.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'] dock atom type numbers: [5, 12, 1, 1, 1, 14, 11, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 8, 1, 16, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 3, 3, 3, 9, 41, 180, 180, 180, 180, 180, 1, 1, 1, 1, 4, 4, 4, 1, 9, 41, 41, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 16, 17, 18, 19, 23, 27] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 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: REAL300025569569 none COC1=CC(S(=O)(=O)NCC2=NC(=O)O[N-]2)=CN=C1Cl 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.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'] dock atom type numbers: [5, 12, 1, 1, 1, 14, 11, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 8, 1, 16, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 180, 180, 180, 117, 55, 117, 117, 8, 1, 1, 1, 1, 1, 1, 1, 180, 180, 180, 180, 201, 201, 201, 180, 55, 8, 8, 180] 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: 618 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901151/working/building/REAL300025569569 /scratch/stefan/7901151/working /scratch/stefan/7901151 Finished preparing REAL300025569569 Recording results /scratch/stefan/7901151/working /scratch/stefan/7901151 Appending to /scratch/stefan/7901151/finished/xaaaaat_worked.* 0: /scratch/stefan/7901151/working/building/REAL300025569569/0.* Removing working files in /scratch/stefan/7901151/working/building/REAL300025569569 Building REAL300025569570 mkdir: created directory `/scratch/stefan/7901151/working/building/REAL300025569570' /scratch/stefan/7901151/working/building/REAL300025569570 /scratch/stefan/7901151/working /scratch/stefan/7901151 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025569570 mkdir: created directory `0' /scratch/stefan/7901151/working/building/REAL300025569570/0 /scratch/stefan/7901151/working/building/REAL300025569570 /scratch/stefan/7901151/working /scratch/stefan/7901151 Protomer 0 (index: 70) Found valid previously generated 3D confromation in /scratch/stefan/7901151/working/3D/70 `/scratch/stefan/7901151/working/3D/70' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C(=O)OC2=CC(S(=O)(=O)NCC3=NC(=O)O[N-]3)=CC=C21) `REAL300025569570.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025569570.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901151/working/building/REAL300025569570/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569570 none CCN1C(=O)OC2=CC(S(=O)(=O)NCC3=NC(=O)O[N-]3)=CC=C21 NO_LONG_NAME dock atom types: ['C.3', '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.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, 5, 8, 1, 11, 12, 1, 1, 1, 14, 11, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 43, 113, 113, 113, 113, 113, 1, 1, 1, 5, 5, 5, 5, 5, 1, 9, 43, 43, 1, 1] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 9, 20, 21, 22, 33, 28] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 29, 30, 31]) total number of confs: 270 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569570 none CCN1C(=O)OC2=CC(S(=O)(=O)NCC3=NC(=O)O[N-]3)=CC=C21 NO_LONG_NAME dock atom types: ['C.3', '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.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, 5, 8, 1, 11, 12, 1, 1, 1, 14, 11, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 6, 6, 4, 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, 113, 113, 113, 113, 113, 113, 113, 81, 45, 81, 81, 8, 1, 1, 1, 1, 1, 1, 1, 113, 113, 113, 201, 201, 201, 201, 201, 113, 45, 8, 8, 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]) total number of confs: 905 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901151/working/building/REAL300025569570 /scratch/stefan/7901151/working /scratch/stefan/7901151 Finished preparing REAL300025569570 Recording results /scratch/stefan/7901151/working /scratch/stefan/7901151 Appending to /scratch/stefan/7901151/finished/xaaaaat_worked.* 0: /scratch/stefan/7901151/working/building/REAL300025569570/0.* Removing working files in /scratch/stefan/7901151/working/building/REAL300025569570 Building REAL300025569571 mkdir: created directory `/scratch/stefan/7901151/working/building/REAL300025569571' /scratch/stefan/7901151/working/building/REAL300025569571 /scratch/stefan/7901151/working /scratch/stefan/7901151 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025569571 mkdir: created directory `0' /scratch/stefan/7901151/working/building/REAL300025569571/0 /scratch/stefan/7901151/working/building/REAL300025569571 /scratch/stefan/7901151/working /scratch/stefan/7901151 Protomer 0 (index: 71) Found valid previously generated 3D confromation in /scratch/stefan/7901151/working/3D/71 `/scratch/stefan/7901151/working/3D/71' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CNS(=O)(=O)C2=CC=C(OCC3CCOC3)C(F)=C2)[N-]O1) `REAL300025569571.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025569571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901151/working/building/REAL300025569571/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569571 none O=C1N=C(CNS(=O)(=O)C2=CC=C(OCC3CCOC3)C(F)=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', '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', 'O.3', 'C.3', 'C.ar', 'F', '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, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 5, 5, 5, 12, 5, 1, 15, 1, 8, 12, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 8, 21, 21, 21, 21, 39, 39, 39, 39, 72, 160, 201, 201, 201, 201, 39, 39, 39, 1, 1, 8, 8, 21, 39, 39, 160, 160, 201, 201, 201, 201, 201, 201, 201, 39] 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: 699 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569571 none O=C1N=C(CNS(=O)(=O)C2=CC=C(OCC3CCOC3)C(F)=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', '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', 'O.3', 'C.3', 'C.ar', 'F', '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, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 5, 5, 5, 12, 5, 1, 15, 1, 8, 12, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 129, 87, 58, 58, 58, 58, 32, 58, 58, 23, 7, 1, 1, 1, 1, 1, 1, 58, 58, 58, 199, 201, 129, 129, 87, 58, 58, 7, 7, 1, 1, 1, 1, 1, 1, 1, 58] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 39]) total number of confs: 681 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569571 none O=C1N=C(CNS(=O)(=O)C2=CC=C(OCC3CCOC3)C(F)=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', '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', 'O.3', 'C.3', 'C.ar', 'F', '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, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 5, 5, 5, 12, 5, 1, 15, 1, 8, 12, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [39, 39, 39, 13, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 8, 37, 58, 58, 58, 58, 1, 1, 1, 39, 39, 13, 13, 5, 1, 1, 37, 37, 58, 58, 58, 58, 58, 58, 58, 1] 201 rigid atoms, others: [6, 39, 9, 10, 11, 12, 13, 20, 21, 22, 28, 29] set([0, 1, 2, 3, 4, 5, 7, 8, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 270 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901151/working/building/REAL300025569571 /scratch/stefan/7901151/working /scratch/stefan/7901151 Finished preparing REAL300025569571 Recording results /scratch/stefan/7901151/working /scratch/stefan/7901151 Appending to /scratch/stefan/7901151/finished/xaaaaat_worked.* 0: /scratch/stefan/7901151/working/building/REAL300025569571/0.* Removing working files in /scratch/stefan/7901151/working/building/REAL300025569571 Building REAL300025569572 mkdir: created directory `/scratch/stefan/7901151/working/building/REAL300025569572' /scratch/stefan/7901151/working/building/REAL300025569572 /scratch/stefan/7901151/working /scratch/stefan/7901151 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025569572 mkdir: created directory `0' /scratch/stefan/7901151/working/building/REAL300025569572/0 /scratch/stefan/7901151/working/building/REAL300025569572 /scratch/stefan/7901151/working /scratch/stefan/7901151 Protomer 0 (index: 72) Found valid previously generated 3D confromation in /scratch/stefan/7901151/working/3D/72 `/scratch/stefan/7901151/working/3D/72' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C2=CC=C(S(=O)(=O)NCC3=NC(=O)O[N-]3)C=C2)OCCO1) `REAL300025569572.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025569572.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901151/working/building/REAL300025569572/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569572 none CC1(C2=CC=C(S(=O)(=O)NCC3=NC(=O)O[N-]3)C=C2)OCCO1 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.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 12, 5, 5, 12, 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, 5, 3, 7, 7, 7, 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, 6, 6, 1, 2, 11, 11, 11, 34, 93, 201, 201, 201, 201, 201, 6, 6, 1, 1, 1, 1, 2, 2, 2, 6, 6, 34, 93, 93, 6, 6, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 35, 36, 33, 34, 19, 20, 21, 22] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 554 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569572 none CC1(C2=CC=C(S(=O)(=O)NCC3=NC(=O)O[N-]3)C=C2)OCCO1 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.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 12, 5, 5, 12, 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, 5, 3, 7, 7, 7, 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, 102, 102, 158, 158, 102, 45, 102, 102, 8, 1, 1, 1, 1, 1, 1, 1, 158, 158, 201, 201, 201, 201, 201, 201, 201, 158, 158, 45, 8, 8, 158, 158, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 1006 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569572 none CC1(C2=CC=C(S(=O)(=O)NCC3=NC(=O)O[N-]3)C=C2)OCCO1 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.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 12, 5, 5, 12, 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, 5, 3, 7, 7, 7, 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: [6, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 46, 158, 158, 158, 158, 158, 1, 1, 6, 6, 6, 6, 6, 6, 6, 1, 1, 9, 46, 46, 1, 1, 6, 6, 6, 6] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 17, 18, 26, 27, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 33, 34, 35, 36]) total number of confs: 321 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901151/working/building/REAL300025569572 /scratch/stefan/7901151/working /scratch/stefan/7901151 Finished preparing REAL300025569572 Recording results /scratch/stefan/7901151/working /scratch/stefan/7901151 Appending to /scratch/stefan/7901151/finished/xaaaaat_worked.* 0: /scratch/stefan/7901151/working/building/REAL300025569572/0.* Removing working files in /scratch/stefan/7901151/working/building/REAL300025569572 Building REAL300025569573 mkdir: created directory `/scratch/stefan/7901151/working/building/REAL300025569573' /scratch/stefan/7901151/working/building/REAL300025569573 /scratch/stefan/7901151/working /scratch/stefan/7901151 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025569573 mkdir: created directory `0' /scratch/stefan/7901151/working/building/REAL300025569573/0 /scratch/stefan/7901151/working/building/REAL300025569573 /scratch/stefan/7901151/working /scratch/stefan/7901151 Protomer 0 (index: 73) Found valid previously generated 3D confromation in /scratch/stefan/7901151/working/3D/73 `/scratch/stefan/7901151/working/3D/73' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CNS(=O)(=O)C2=CC(Br)=CC3=C2OCC3)[N-]O1) `REAL300025569573.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025569573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901151/working/building/REAL300025569573/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569573 none O=C1N=C(CNS(=O)(=O)C2=CC(Br)=CC3=C2OCC3)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 8, 14, 11, 11, 1, 1, 1, 17, 1, 1, 1, 12, 5, 5, 8, 12, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 167 conformations in input total number of sets (complete confs): 167 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 9, 52, 117, 117, 117, 167, 167, 167, 167, 167, 167, 167, 167, 167, 1, 1, 9, 9, 52, 167, 167, 167, 167, 167, 167] 167 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: 537 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569573 none O=C1N=C(CNS(=O)(=O)C2=CC(Br)=CC3=C2OCC3)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 8, 14, 11, 11, 1, 1, 1, 17, 1, 1, 1, 12, 5, 5, 8, 12, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 167 conformations in input total number of sets (complete confs): 167 using faster count positions algorithm for large data unique positions, atoms: [167, 167, 167, 85, 25, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 167, 167, 85, 85, 25, 1, 1, 1, 1, 1, 1] 167 rigid atoms, others: [6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 7, 8, 19, 20, 21, 22, 23]) total number of confs: 457 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901151/working/building/REAL300025569573 /scratch/stefan/7901151/working /scratch/stefan/7901151 Finished preparing REAL300025569573 Recording results /scratch/stefan/7901151/working /scratch/stefan/7901151 Appending to /scratch/stefan/7901151/finished/xaaaaat_worked.* 0: /scratch/stefan/7901151/working/building/REAL300025569573/0.* Removing working files in /scratch/stefan/7901151/working/building/REAL300025569573 Building REAL300025569574 mkdir: created directory `/scratch/stefan/7901151/working/building/REAL300025569574' /scratch/stefan/7901151/working/building/REAL300025569574 /scratch/stefan/7901151/working /scratch/stefan/7901151 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025569574 mkdir: created directory `0' /scratch/stefan/7901151/working/building/REAL300025569574/0 /scratch/stefan/7901151/working/building/REAL300025569574 /scratch/stefan/7901151/working /scratch/stefan/7901151 Protomer 0 (index: 74) Found valid previously generated 3D confromation in /scratch/stefan/7901151/working/3D/74 `/scratch/stefan/7901151/working/3D/74' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CNS(=O)(=O)C2=CC=C(I)C=C2)[N-]O1) `REAL300025569574.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025569574.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901151/working/building/REAL300025569574/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569574 none O=C1N=C(CNS(=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', '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'] dock atom type numbers: [11, 1, 8, 1, 5, 8, 14, 11, 11, 1, 1, 1, 1, 18, 1, 1, 8, 12, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 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, 36, 55, 55, 55, 55, 55, 55, 55, 55, 55, 1, 1, 9, 9, 36, 55, 55, 55, 55] 55 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: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569574 none O=C1N=C(CNS(=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', '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'] dock atom type numbers: [11, 1, 8, 1, 5, 8, 14, 11, 11, 1, 1, 1, 1, 18, 1, 1, 8, 12, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 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, 25, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 55, 55, 25, 25, 5, 1, 1, 1, 1] 55 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 16, 17, 18, 19, 20]) total number of confs: 129 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901151/working/building/REAL300025569574 /scratch/stefan/7901151/working /scratch/stefan/7901151 Finished preparing REAL300025569574 Recording results /scratch/stefan/7901151/working /scratch/stefan/7901151 Appending to /scratch/stefan/7901151/finished/xaaaaat_worked.* 0: /scratch/stefan/7901151/working/building/REAL300025569574/0.* Removing working files in /scratch/stefan/7901151/working/building/REAL300025569574 Building REAL300025569575 mkdir: created directory `/scratch/stefan/7901151/working/building/REAL300025569575' /scratch/stefan/7901151/working/building/REAL300025569575 /scratch/stefan/7901151/working /scratch/stefan/7901151 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025569575 mkdir: created directory `0' /scratch/stefan/7901151/working/building/REAL300025569575/0 /scratch/stefan/7901151/working/building/REAL300025569575 /scratch/stefan/7901151/working /scratch/stefan/7901151 Protomer 0 (index: 75) Found valid previously generated 3D confromation in /scratch/stefan/7901151/working/3D/75 `/scratch/stefan/7901151/working/3D/75' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC([N+](=O)[O-])=C(C)C(S(=O)(=O)NCC2=NC(=O)O[N-]2)=C1) `REAL300025569575.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025569575.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901151/working/building/REAL300025569575/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569575 none CC1=CC([N+](=O)[O-])=C(C)C(S(=O)(=O)NCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 8, 11, 11, 1, 5, 1, 14, 11, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 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, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 3, 3, 3, 5, 21, 55, 55, 55, 55, 55, 1, 2, 2, 2, 1, 2, 2, 2, 5, 21, 21, 1] 55 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 32, 21, 25] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 26, 27, 28, 29, 30, 31]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569575 none CC1=CC([N+](=O)[O-])=C(C)C(S(=O)(=O)NCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 8, 11, 11, 1, 5, 1, 14, 11, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 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, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 33, 55, 55, 8, 1, 1, 1, 1, 1, 1, 1, 55, 55, 55, 55, 55, 55, 55, 55, 33, 8, 8, 55] 55 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: 217 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901151/working/building/REAL300025569575 /scratch/stefan/7901151/working /scratch/stefan/7901151 Finished preparing REAL300025569575 Recording results /scratch/stefan/7901151/working /scratch/stefan/7901151 Appending to /scratch/stefan/7901151/finished/xaaaaat_worked.* 0: /scratch/stefan/7901151/working/building/REAL300025569575/0.* Removing working files in /scratch/stefan/7901151/working/building/REAL300025569575 Building REAL300025569576 mkdir: created directory `/scratch/stefan/7901151/working/building/REAL300025569576' /scratch/stefan/7901151/working/building/REAL300025569576 /scratch/stefan/7901151/working /scratch/stefan/7901151 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025569576 mkdir: created directory `0' /scratch/stefan/7901151/working/building/REAL300025569576/0 /scratch/stefan/7901151/working/building/REAL300025569576 /scratch/stefan/7901151/working /scratch/stefan/7901151 Protomer 0 (index: 76) Found valid previously generated 3D confromation in /scratch/stefan/7901151/working/3D/76 `/scratch/stefan/7901151/working/3D/76' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CNS(=O)(=O)CCCN2C(=O)C3=CC=CC=C3C2=O)[N-]O1) `REAL300025569576.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025569576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901151/working/building/REAL300025569576/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569576 none O=C1N=C(CNS(=O)(=O)CCCN2C(=O)C3=CC=CC=C3C2=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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, 8, 14, 11, 11, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 8, 12, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 5, 7, 9, 9, 9, 26, 38, 48, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 1, 1, 5, 5, 7, 26, 26, 38, 38, 48, 48, 49, 49, 49, 49] 49 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]) 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: REAL300025569576 none O=C1N=C(CNS(=O)(=O)CCCN2C(=O)C3=CC=CC=C3C2=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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, 8, 14, 11, 11, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 8, 12, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 49, 38, 38, 29, 13, 29, 29, 7, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 49, 49, 38, 38, 38, 12, 12, 9, 9, 4, 4, 1, 1, 1, 1] 49 rigid atoms, others: [34, 35, 36, 37, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 196 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901151/working/building/REAL300025569576 /scratch/stefan/7901151/working /scratch/stefan/7901151 Finished preparing REAL300025569576 Recording results /scratch/stefan/7901151/working /scratch/stefan/7901151 Appending to /scratch/stefan/7901151/finished/xaaaaat_worked.* 0: /scratch/stefan/7901151/working/building/REAL300025569576/0.* Removing working files in /scratch/stefan/7901151/working/building/REAL300025569576 Building REAL300025569577 mkdir: created directory `/scratch/stefan/7901151/working/building/REAL300025569577' /scratch/stefan/7901151/working/building/REAL300025569577 /scratch/stefan/7901151/working /scratch/stefan/7901151 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025569577 mkdir: created directory `0' /scratch/stefan/7901151/working/building/REAL300025569577/0 /scratch/stefan/7901151/working/building/REAL300025569577 /scratch/stefan/7901151/working /scratch/stefan/7901151 Protomer 0 (index: 77) Found valid previously generated 3D confromation in /scratch/stefan/7901151/working/3D/77 `/scratch/stefan/7901151/working/3D/77' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=NOC2=NC=C(S(=O)(=O)NCC3=NC(=O)O[N-]3)C=C12) `REAL300025569577.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025569577.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901151/working/building/REAL300025569577/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569577 none CCC1=NOC2=NC=C(S(=O)(=O)NCC3=NC(=O)O[N-]3)C=C12 NO_LONG_NAME dock atom types: ['C.3', '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.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, 5, 1, 8, 12, 1, 8, 1, 1, 14, 11, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 37, 141, 141, 141, 141, 141, 1, 1, 5, 5, 5, 5, 5, 1, 9, 37, 37, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 20, 21, 27, 31] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 28, 29, 30]) total number of confs: 280 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569577 none CCC1=NOC2=NC=C(S(=O)(=O)NCC3=NC(=O)O[N-]3)C=C12 NO_LONG_NAME dock atom types: ['C.3', '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.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, 5, 1, 8, 12, 1, 8, 1, 1, 14, 11, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 6, 4, 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, 141, 141, 141, 141, 141, 141, 141, 97, 49, 97, 97, 8, 1, 1, 1, 1, 1, 1, 1, 141, 141, 201, 201, 201, 201, 201, 141, 49, 8, 8, 141] 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: 832 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901151/working/building/REAL300025569577 /scratch/stefan/7901151/working /scratch/stefan/7901151 Finished preparing REAL300025569577 Recording results /scratch/stefan/7901151/working /scratch/stefan/7901151 Appending to /scratch/stefan/7901151/finished/xaaaaat_worked.* 0: /scratch/stefan/7901151/working/building/REAL300025569577/0.* Removing working files in /scratch/stefan/7901151/working/building/REAL300025569577 Building REAL300025569578 mkdir: created directory `/scratch/stefan/7901151/working/building/REAL300025569578' /scratch/stefan/7901151/working/building/REAL300025569578 /scratch/stefan/7901151/working /scratch/stefan/7901151 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025569578 mkdir: created directory `0' /scratch/stefan/7901151/working/building/REAL300025569578/0 /scratch/stefan/7901151/working/building/REAL300025569578 /scratch/stefan/7901151/working /scratch/stefan/7901151 Protomer 0 (index: 78) Found valid previously generated 3D confromation in /scratch/stefan/7901151/working/3D/78 `/scratch/stefan/7901151/working/3D/78' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CNS(=O)(=O)C2=CC=CC=C2[N+](=O)[O-])[N-]O1) `REAL300025569578.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025569578.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901151/working/building/REAL300025569578/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569578 none O=C1N=C(CNS(=O)(=O)C2=CC=CC=C2[N+](=O)[O-])[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', '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', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 8, 11, 11, 8, 12, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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, 43, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 1, 1, 9, 9, 43, 45, 45, 45, 45] 45 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: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569578 none O=C1N=C(CNS(=O)(=O)C2=CC=CC=C2[N+](=O)[O-])[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', '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', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 8, 11, 11, 8, 12, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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, 19, 5, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 45, 45, 19, 19, 5, 1, 1, 1, 1] 45 rigid atoms, others: [6, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 7, 8, 16, 17, 18, 19, 20, 21, 22]) total number of confs: 116 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901151/working/building/REAL300025569578 /scratch/stefan/7901151/working /scratch/stefan/7901151 Finished preparing REAL300025569578 Recording results /scratch/stefan/7901151/working /scratch/stefan/7901151 Appending to /scratch/stefan/7901151/finished/xaaaaat_worked.* 0: /scratch/stefan/7901151/working/building/REAL300025569578/0.* Removing working files in /scratch/stefan/7901151/working/building/REAL300025569578 Building REAL300025569579 mkdir: created directory `/scratch/stefan/7901151/working/building/REAL300025569579' /scratch/stefan/7901151/working/building/REAL300025569579 /scratch/stefan/7901151/working /scratch/stefan/7901151 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025569579 mkdir: created directory `0' /scratch/stefan/7901151/working/building/REAL300025569579/0 /scratch/stefan/7901151/working/building/REAL300025569579 /scratch/stefan/7901151/working /scratch/stefan/7901151 Protomer 0 (index: 79) Found valid previously generated 3D confromation in /scratch/stefan/7901151/working/3D/79 `/scratch/stefan/7901151/working/3D/79' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CNS(=O)(=O)C2=CC=C(Br)O2)[N-]O1) `REAL300025569579.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025569579.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901151/working/building/REAL300025569579/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569579 none O=C1N=C(CNS(=O)(=O)C2=CC=C(Br)O2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'O.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 8, 14, 11, 11, 1, 1, 1, 1, 17, 12, 8, 12, 7, 7, 6, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7] 0 hydrogens need rotated 167 conformations in input total number of sets (complete confs): 167 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 9, 53, 127, 127, 127, 167, 167, 167, 167, 167, 1, 1, 9, 9, 53, 167, 167] 167 rigid atoms, others: [0, 1, 2, 3, 4, 15, 16] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 17, 18, 19, 20, 21]) 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: REAL300025569579 none O=C1N=C(CNS(=O)(=O)C2=CC=C(Br)O2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'O.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 8, 14, 11, 11, 1, 1, 1, 1, 17, 12, 8, 12, 7, 7, 6, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7] 0 hydrogens need rotated 167 conformations in input total number of sets (complete confs): 167 using faster count positions algorithm for large data unique positions, atoms: [167, 167, 167, 92, 23, 6, 1, 6, 6, 1, 1, 1, 1, 1, 1, 167, 167, 92, 92, 23, 1, 1] 167 rigid atoms, others: [6, 9, 10, 11, 12, 13, 14, 20, 21] set([0, 1, 2, 3, 4, 5, 7, 8, 15, 16, 17, 18, 19]) total number of confs: 459 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901151/working/building/REAL300025569579 /scratch/stefan/7901151/working /scratch/stefan/7901151 mkdir: created directory `1' /scratch/stefan/7901151/working/building/REAL300025569579/1 /scratch/stefan/7901151/working/building/REAL300025569579 /scratch/stefan/7901151/working /scratch/stefan/7901151 Protomer 1 (index: 80) Found valid previously generated 3D confromation in /scratch/stefan/7901151/working/3D/80 `/scratch/stefan/7901151/working/3D/80' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(C[N-]S(=O)(=O)C2=CC=C(Br)O2)[N-]O1) `REAL300025569579.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025569579.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901151/working/building/REAL300025569579/1/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: REAL300025569579 none O=C1N=C(C[N-]S(=O)(=O)C2=CC=C(Br)O2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'O.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 8, 14, 11, 11, 1, 1, 1, 1, 17, 12, 8, 12, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7] 0 hydrogens need rotated 81 conformations in input total number of sets (complete confs): 81 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 9, 31, 63, 63, 63, 81, 81, 81, 81, 81, 1, 1, 9, 9, 81, 81] 81 rigid atoms, others: [0, 1, 2, 3, 4, 15, 16] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 17, 18, 19, 20]) total number of confs: 250 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569579 none O=C1N=C(C[N-]S(=O)(=O)C2=CC=C(Br)O2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'O.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 8, 14, 11, 11, 1, 1, 1, 1, 17, 12, 8, 12, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7] 0 hydrogens need rotated 81 conformations in input total number of sets (complete confs): 81 using faster count positions algorithm for large data unique positions, atoms: [81, 81, 81, 55, 23, 6, 1, 6, 6, 1, 1, 1, 1, 1, 1, 81, 81, 55, 55, 1, 1] 81 rigid atoms, others: [6, 9, 10, 11, 12, 13, 14, 19, 20] set([0, 1, 2, 3, 4, 5, 7, 8, 15, 16, 17, 18]) total number of confs: 230 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901151/working/building/REAL300025569579 /scratch/stefan/7901151/working /scratch/stefan/7901151 Finished preparing REAL300025569579 Recording results /scratch/stefan/7901151/working /scratch/stefan/7901151 Appending to /scratch/stefan/7901151/finished/xaaaaat_worked.* 0: /scratch/stefan/7901151/working/building/REAL300025569579/0.* 1: /scratch/stefan/7901151/working/building/REAL300025569579/1.* Removing working files in /scratch/stefan/7901151/working/building/REAL300025569579 Building REAL300025569580 mkdir: created directory `/scratch/stefan/7901151/working/building/REAL300025569580' /scratch/stefan/7901151/working/building/REAL300025569580 /scratch/stefan/7901151/working /scratch/stefan/7901151 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025569580 mkdir: created directory `0' /scratch/stefan/7901151/working/building/REAL300025569580/0 /scratch/stefan/7901151/working/building/REAL300025569580 /scratch/stefan/7901151/working /scratch/stefan/7901151 Protomer 0 (index: 81) Found valid previously generated 3D confromation in /scratch/stefan/7901151/working/3D/81 `/scratch/stefan/7901151/working/3D/81' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1(CS(=O)(=O)NCC2=NC(=O)O[N-]2)CCCCC1) `REAL300025569580.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025569580.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901151/working/building/REAL300025569580/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569580 none N#CC1(CS(=O)(=O)NCC2=NC(=O)O[N-]2)CCCCC1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 5, 14, 11, 11, 8, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 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, 8, 16, 16, 16, 46, 111, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 8, 8, 46, 111, 111, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 33, 32, 34, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24]) total number of confs: 606 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569580 none N#CC1(CS(=O)(=O)NCC2=NC(=O)O[N-]2)CCCCC1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 5, 14, 11, 11, 8, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 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, 155, 90, 58, 90, 90, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 155, 155, 58, 8, 8, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 841 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901151/working/building/REAL300025569580 /scratch/stefan/7901151/working /scratch/stefan/7901151 Finished preparing REAL300025569580 Recording results /scratch/stefan/7901151/working /scratch/stefan/7901151 Appending to /scratch/stefan/7901151/finished/xaaaaat_worked.* 0: /scratch/stefan/7901151/working/building/REAL300025569580/0.* Removing working files in /scratch/stefan/7901151/working/building/REAL300025569580 Building REAL300025569581 mkdir: created directory `/scratch/stefan/7901151/working/building/REAL300025569581' /scratch/stefan/7901151/working/building/REAL300025569581 /scratch/stefan/7901151/working /scratch/stefan/7901151 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025569581 mkdir: created directory `0' /scratch/stefan/7901151/working/building/REAL300025569581/0 /scratch/stefan/7901151/working/building/REAL300025569581 /scratch/stefan/7901151/working /scratch/stefan/7901151 Protomer 0 (index: 82) Found valid previously generated 3D confromation in /scratch/stefan/7901151/working/3D/82 `/scratch/stefan/7901151/working/3D/82' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CNS(=O)(=O)C2=C(F)C=CC=C2Cl)[N-]O1) `REAL300025569581.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025569581.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901151/working/building/REAL300025569581/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569581 none O=C1N=C(CNS(=O)(=O)C2=C(F)C=CC=C2Cl)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 8, 14, 11, 11, 1, 1, 15, 1, 1, 1, 1, 16, 8, 12, 7, 7, 6, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 4, 7, 6, 6, 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, 56, 97, 97, 97, 134, 134, 134, 134, 134, 134, 134, 1, 1, 9, 9, 56, 134, 134, 134] 134 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]) 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: REAL300025569581 none O=C1N=C(CNS(=O)(=O)C2=C(F)C=CC=C2Cl)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 8, 14, 11, 11, 1, 1, 15, 1, 1, 1, 1, 16, 8, 12, 7, 7, 6, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 4, 7, 6, 6, 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, 66, 23, 9, 1, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 134, 134, 66, 66, 23, 1, 1, 1] 134 rigid atoms, others: [6, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 7, 8, 17, 18, 19, 20, 21]) total number of confs: 359 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901151/working/building/REAL300025569581 /scratch/stefan/7901151/working /scratch/stefan/7901151 mkdir: created directory `1' /scratch/stefan/7901151/working/building/REAL300025569581/1 /scratch/stefan/7901151/working/building/REAL300025569581 /scratch/stefan/7901151/working /scratch/stefan/7901151 Protomer 1 (index: 83) Found valid previously generated 3D confromation in /scratch/stefan/7901151/working/3D/83 `/scratch/stefan/7901151/working/3D/83' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(C[N-]S(=O)(=O)C2=C(F)C=CC=C2Cl)[N-]O1) `REAL300025569581.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025569581.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901151/working/building/REAL300025569581/1/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: REAL300025569581 none O=C1N=C(C[N-]S(=O)(=O)C2=C(F)C=CC=C2Cl)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 8, 14, 11, 11, 1, 1, 15, 1, 1, 1, 1, 16, 8, 12, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7] 0 hydrogens need rotated 93 conformations in input total number of sets (complete confs): 93 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 9, 34, 73, 73, 73, 93, 93, 93, 79, 93, 93, 93, 1, 1, 9, 9, 93, 93, 93] 93 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]) 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: REAL300025569581 none O=C1N=C(C[N-]S(=O)(=O)C2=C(F)C=CC=C2Cl)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 8, 14, 11, 11, 1, 1, 15, 1, 1, 1, 1, 16, 8, 12, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7] 0 hydrogens need rotated 93 conformations in input total number of sets (complete confs): 93 using faster count positions algorithm for large data unique positions, atoms: [93, 93, 93, 60, 24, 11, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 93, 93, 60, 60, 1, 1, 1] 93 rigid atoms, others: [6, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 7, 8, 17, 18, 19, 20]) total number of confs: 270 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901151/working/building/REAL300025569581 /scratch/stefan/7901151/working /scratch/stefan/7901151 Finished preparing REAL300025569581 Recording results /scratch/stefan/7901151/working /scratch/stefan/7901151 Appending to /scratch/stefan/7901151/finished/xaaaaat_worked.* 0: /scratch/stefan/7901151/working/building/REAL300025569581/0.* 1: /scratch/stefan/7901151/working/building/REAL300025569581/1.* Removing working files in /scratch/stefan/7901151/working/building/REAL300025569581 Building REAL300025569582 mkdir: created directory `/scratch/stefan/7901151/working/building/REAL300025569582' /scratch/stefan/7901151/working/building/REAL300025569582 /scratch/stefan/7901151/working /scratch/stefan/7901151 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025569582 mkdir: created directory `0' /scratch/stefan/7901151/working/building/REAL300025569582/0 /scratch/stefan/7901151/working/building/REAL300025569582 /scratch/stefan/7901151/working /scratch/stefan/7901151 Protomer 0 (index: 84) Found valid previously generated 3D confromation in /scratch/stefan/7901151/working/3D/84 `/scratch/stefan/7901151/working/3D/84' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(S(=O)(=O)NCC2=NC(=O)O[N-]2)C(Cl)=N1) `REAL300025569582.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025569582.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901151/working/building/REAL300025569582/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569582 none CC1=CC=C(S(=O)(=O)NCC2=NC(=O)O[N-]2)C(Cl)=N1 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.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'Cl', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 16, 8, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 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, 1, 7, 7, 7, 15, 43, 91, 91, 91, 91, 91, 1, 1, 1, 2, 2, 2, 1, 1, 15, 43, 43] 91 rigid atoms, others: [0, 1, 2, 3, 4, 5, 16, 17, 18, 22, 23] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 24, 25, 26]) total number of confs: 242 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569582 none CC1=CC=C(S(=O)(=O)NCC2=NC(=O)O[N-]2)C(Cl)=N1 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.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'Cl', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 16, 8, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 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, 91, 79, 47, 79, 79, 8, 1, 1, 1, 1, 1, 1, 1, 91, 91, 91, 91, 91, 91, 91, 91, 47, 8, 8] 91 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 317 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901151/working/building/REAL300025569582 /scratch/stefan/7901151/working /scratch/stefan/7901151 Finished preparing REAL300025569582 Recording results /scratch/stefan/7901151/working /scratch/stefan/7901151 Appending to /scratch/stefan/7901151/finished/xaaaaat_worked.* 0: /scratch/stefan/7901151/working/building/REAL300025569582/0.* Removing working files in /scratch/stefan/7901151/working/building/REAL300025569582 Building REAL300025569583 mkdir: created directory `/scratch/stefan/7901151/working/building/REAL300025569583' /scratch/stefan/7901151/working/building/REAL300025569583 /scratch/stefan/7901151/working /scratch/stefan/7901151 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025569583 mkdir: created directory `0' /scratch/stefan/7901151/working/building/REAL300025569583/0 /scratch/stefan/7901151/working/building/REAL300025569583 /scratch/stefan/7901151/working /scratch/stefan/7901151 Protomer 0 (index: 85) Found valid previously generated 3D confromation in /scratch/stefan/7901151/working/3D/85 `/scratch/stefan/7901151/working/3D/85' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C#N)=CC=C1S(=O)(=O)NCC1=NC(=O)O[N-]1) `REAL300025569583.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025569583.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901151/working/building/REAL300025569583/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569583 none COC1=CC(C#N)=CC=C1S(=O)(=O)NCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.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.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, 1, 8, 1, 1, 1, 14, 11, 11, 8, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 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: [4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 24, 79, 196, 196, 196, 196, 196, 4, 4, 4, 1, 1, 1, 24, 79, 79] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 24, 25, 26] set([0, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29]) total number of confs: 466 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569583 none COC1=CC(C#N)=CC=C1S(=O)(=O)NCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.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.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, 1, 8, 1, 1, 1, 14, 11, 11, 8, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 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, 196, 196, 196, 196, 196, 196, 196, 196, 120, 55, 120, 120, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 196, 196, 196, 55, 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: 595 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901151/working/building/REAL300025569583 /scratch/stefan/7901151/working /scratch/stefan/7901151 Finished preparing REAL300025569583 Recording results /scratch/stefan/7901151/working /scratch/stefan/7901151 Appending to /scratch/stefan/7901151/finished/xaaaaat_worked.* 0: /scratch/stefan/7901151/working/building/REAL300025569583/0.* Removing working files in /scratch/stefan/7901151/working/building/REAL300025569583 Building REAL300025569584 mkdir: created directory `/scratch/stefan/7901151/working/building/REAL300025569584' /scratch/stefan/7901151/working/building/REAL300025569584 /scratch/stefan/7901151/working /scratch/stefan/7901151 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025569584 mkdir: created directory `0' /scratch/stefan/7901151/working/building/REAL300025569584/0 /scratch/stefan/7901151/working/building/REAL300025569584 /scratch/stefan/7901151/working /scratch/stefan/7901151 Protomer 0 (index: 86) Found valid previously generated 3D confromation in /scratch/stefan/7901151/working/3D/86 `/scratch/stefan/7901151/working/3D/86' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CNS(=O)(=O)C2=CC=C([N+](=O)[O-])C3=CC=CN=C32)[N-]O1) `REAL300025569584.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025569584.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901151/working/building/REAL300025569584/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569584 none O=C1N=C(CNS(=O)(=O)C2=CC=C([N+](=O)[O-])C3=CC=CN=C32)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', '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.ar', 'C.ar', 'N.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 8, 1, 8, 12, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 141 conformations in input total number of sets (complete confs): 141 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 9, 55, 106, 106, 106, 141, 141, 141, 141, 141, 141, 141, 141, 141, 141, 141, 141, 1, 1, 9, 9, 55, 141, 141, 141, 141, 141] 141 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: 461 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569584 none O=C1N=C(CNS(=O)(=O)C2=CC=C([N+](=O)[O-])C3=CC=CN=C32)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', '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.ar', 'C.ar', 'N.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 8, 1, 8, 12, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 141 conformations in input total number of sets (complete confs): 141 using faster count positions algorithm for large data unique positions, atoms: [141, 141, 141, 72, 23, 7, 1, 7, 7, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 141, 141, 72, 72, 23, 1, 1, 1, 1, 1] 141 rigid atoms, others: [6, 9, 10, 11, 12, 13, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 8, 14, 15, 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/7901151/working/building/REAL300025569584 /scratch/stefan/7901151/working /scratch/stefan/7901151 Finished preparing REAL300025569584 Recording results /scratch/stefan/7901151/working /scratch/stefan/7901151 Appending to /scratch/stefan/7901151/finished/xaaaaat_worked.* 0: /scratch/stefan/7901151/working/building/REAL300025569584/0.* Removing working files in /scratch/stefan/7901151/working/building/REAL300025569584 Building REAL300025569585 mkdir: created directory `/scratch/stefan/7901151/working/building/REAL300025569585' /scratch/stefan/7901151/working/building/REAL300025569585 /scratch/stefan/7901151/working /scratch/stefan/7901151 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025569585 mkdir: created directory `0' /scratch/stefan/7901151/working/building/REAL300025569585/0 /scratch/stefan/7901151/working/building/REAL300025569585 /scratch/stefan/7901151/working /scratch/stefan/7901151 Protomer 0 (index: 87) Found valid previously generated 3D confromation in /scratch/stefan/7901151/working/3D/87 `/scratch/stefan/7901151/working/3D/87' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSC1=CC=C(S(=O)(=O)NCC2=NC(=O)O[N-]2)C=C1Cl) `REAL300025569585.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025569585.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901151/working/building/REAL300025569585/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569585 none CSC1=CC=C(S(=O)(=O)NCC2=NC(=O)O[N-]2)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 35, 143, 143, 143, 143, 143, 1, 1, 1, 8, 8, 8, 1, 1, 9, 35, 35, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 17, 18, 19, 23, 24, 28] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 25, 26, 27]) total number of confs: 275 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569585 none CSC1=CC=C(S(=O)(=O)NCC2=NC(=O)O[N-]2)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 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, 143, 143, 143, 143, 86, 51, 86, 86, 8, 1, 1, 1, 1, 1, 1, 1, 143, 143, 143, 201, 201, 201, 143, 143, 51, 8, 8, 143] 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: 555 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901151/working/building/REAL300025569585 /scratch/stefan/7901151/working /scratch/stefan/7901151 Finished preparing REAL300025569585 Recording results /scratch/stefan/7901151/working /scratch/stefan/7901151 Appending to /scratch/stefan/7901151/finished/xaaaaat_worked.* 0: /scratch/stefan/7901151/working/building/REAL300025569585/0.* Removing working files in /scratch/stefan/7901151/working/building/REAL300025569585 Building REAL300025569586 mkdir: created directory `/scratch/stefan/7901151/working/building/REAL300025569586' /scratch/stefan/7901151/working/building/REAL300025569586 /scratch/stefan/7901151/working /scratch/stefan/7901151 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025569586 mkdir: created directory `0' /scratch/stefan/7901151/working/building/REAL300025569586/0 /scratch/stefan/7901151/working/building/REAL300025569586 /scratch/stefan/7901151/working /scratch/stefan/7901151 Protomer 0 (index: 88) Found valid previously generated 3D confromation in /scratch/stefan/7901151/working/3D/88 `/scratch/stefan/7901151/working/3D/88' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CNS(=O)(=O)C2=CC=C(N3C=CC=C3)C=C2)[N-]O1) `REAL300025569586.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025569586.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901151/working/building/REAL300025569586/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569586 none O=C1N=C(CNS(=O)(=O)C2=CC=C(N3C=CC=C3)C=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.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, 8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 12, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 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 92 conformations in input total number of sets (complete confs): 92 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 9, 48, 92, 92, 92, 92, 92, 92, 92, 92, 92, 92, 92, 92, 92, 1, 1, 9, 9, 48, 92, 92, 92, 92, 92, 92, 92, 92] 92 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: 344 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569586 none O=C1N=C(CNS(=O)(=O)C2=CC=C(N3C=CC=C3)C=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.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, 8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 12, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 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 92 conformations in input total number of sets (complete confs): 92 using faster count positions algorithm for large data unique positions, atoms: [92, 92, 92, 40, 20, 8, 8, 8, 8, 2, 8, 8, 1, 1, 1, 1, 1, 1, 8, 8, 92, 92, 40, 40, 20, 8, 8, 1, 1, 1, 1, 8, 8] 92 rigid atoms, others: [12, 13, 14, 15, 16, 17, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32]) total number of confs: 229 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569586 none O=C1N=C(CNS(=O)(=O)C2=CC=C(N3C=CC=C3)C=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.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, 8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 12, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 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 92 conformations in input total number of sets (complete confs): 92 using faster count positions algorithm for large data unique positions, atoms: [92, 92, 92, 23, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 92, 92, 23, 23, 5, 1, 1, 5, 5, 5, 5, 1, 1] 92 rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 11, 12, 13, 18, 19, 25, 26, 31] set([0, 1, 2, 3, 4, 14, 15, 16, 17, 20, 21, 22, 23, 24, 27, 28, 29, 30]) total number of confs: 173 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901151/working/building/REAL300025569586 /scratch/stefan/7901151/working /scratch/stefan/7901151 Finished preparing REAL300025569586 Recording results /scratch/stefan/7901151/working /scratch/stefan/7901151 Appending to /scratch/stefan/7901151/finished/xaaaaat_worked.* 0: /scratch/stefan/7901151/working/building/REAL300025569586/0.* Removing working files in /scratch/stefan/7901151/working/building/REAL300025569586 Building REAL300025569587 mkdir: created directory `/scratch/stefan/7901151/working/building/REAL300025569587' /scratch/stefan/7901151/working/building/REAL300025569587 /scratch/stefan/7901151/working /scratch/stefan/7901151 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025569587 mkdir: created directory `0' /scratch/stefan/7901151/working/building/REAL300025569587/0 /scratch/stefan/7901151/working/building/REAL300025569587 /scratch/stefan/7901151/working /scratch/stefan/7901151 Protomer 0 (index: 89) Found valid previously generated 3D confromation in /scratch/stefan/7901151/working/3D/89 `/scratch/stefan/7901151/working/3D/89' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CNS(=O)(=O)C2=CC=C(C(F)(F)F)N=C2)[N-]O1) `REAL300025569587.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025569587.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901151/working/building/REAL300025569587/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569587 none O=C1N=C(CNS(=O)(=O)C2=CC=C(C(F)(F)F)N=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'N.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 8, 14, 11, 11, 1, 1, 1, 1, 5, 15, 15, 15, 8, 1, 8, 12, 7, 7, 6, 7, 7, 7] dock color type numbers: [5, 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] 0 hydrogens need rotated 99 conformations in input total number of sets (complete confs): 99 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 9, 42, 73, 73, 73, 99, 99, 99, 99, 99, 99, 99, 99, 99, 1, 1, 9, 9, 42, 99, 99, 99] 99 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: 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: REAL300025569587 none O=C1N=C(CNS(=O)(=O)C2=CC=C(C(F)(F)F)N=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'N.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 8, 14, 11, 11, 1, 1, 1, 1, 5, 15, 15, 15, 8, 1, 8, 12, 7, 7, 6, 7, 7, 7] dock color type numbers: [5, 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] 0 hydrogens need rotated 99 conformations in input total number of sets (complete confs): 99 using faster count positions algorithm for large data unique positions, atoms: [99, 99, 99, 45, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 99, 99, 45, 45, 9, 1, 1, 1] 99 rigid atoms, others: [6, 9, 10, 11, 12, 13, 17, 18, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 7, 8, 14, 15, 16, 19, 20, 21, 22, 23]) total number of confs: 248 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901151/working/building/REAL300025569587 /scratch/stefan/7901151/working /scratch/stefan/7901151 Finished preparing REAL300025569587 Recording results /scratch/stefan/7901151/working /scratch/stefan/7901151 Appending to /scratch/stefan/7901151/finished/xaaaaat_worked.* 0: /scratch/stefan/7901151/working/building/REAL300025569587/0.* Removing working files in /scratch/stefan/7901151/working/building/REAL300025569587 Building REAL300025569588 mkdir: created directory `/scratch/stefan/7901151/working/building/REAL300025569588' /scratch/stefan/7901151/working/building/REAL300025569588 /scratch/stefan/7901151/working /scratch/stefan/7901151 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025569588 mkdir: created directory `0' /scratch/stefan/7901151/working/building/REAL300025569588/0 /scratch/stefan/7901151/working/building/REAL300025569588 /scratch/stefan/7901151/working /scratch/stefan/7901151 Protomer 0 (index: 90) Found valid previously generated 3D confromation in /scratch/stefan/7901151/working/3D/90 `/scratch/stefan/7901151/working/3D/90' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=C(S(=O)(=O)[N-]CC2=NC(=O)O[N-]2)SC=N1) `REAL300025569588.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025569588.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901151/working/building/REAL300025569588/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569588 none COC(=O)C1=C(S(=O)(=O)[N-]CC2=NC(=O)O[N-]2)SC=N1 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.2', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 14, 11, 11, 8, 5, 1, 8, 1, 11, 12, 8, 14, 1, 8, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 3, 3, 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, 11, 11, 11, 29, 72, 149, 149, 149, 149, 149, 1, 1, 1, 11, 11, 11, 72, 72, 1] 201 rigid atoms, others: [2, 4, 5, 6, 17, 18, 19, 25] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24]) 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: REAL300025569588 none COC(=O)C1=C(S(=O)(=O)[N-]CC2=NC(=O)O[N-]2)SC=N1 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.2', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 14, 11, 11, 8, 5, 1, 8, 1, 11, 12, 8, 14, 1, 8, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 3, 3, 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, 149, 201, 149, 75, 31, 75, 75, 8, 1, 1, 1, 1, 1, 1, 1, 149, 149, 149, 201, 201, 201, 8, 8, 149] 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]) total number of confs: 580 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901151/working/building/REAL300025569588 /scratch/stefan/7901151/working /scratch/stefan/7901151 mkdir: created directory `1' /scratch/stefan/7901151/working/building/REAL300025569588/1 /scratch/stefan/7901151/working/building/REAL300025569588 /scratch/stefan/7901151/working /scratch/stefan/7901151 Protomer 1 (index: 91) Found valid previously generated 3D confromation in /scratch/stefan/7901151/working/3D/91 `/scratch/stefan/7901151/working/3D/91' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=C(S(=O)(=O)NCC2=NC(=O)O[N-]2)SC=N1) `REAL300025569588.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025569588.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901151/working/building/REAL300025569588/1/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: REAL300025569588 none COC(=O)C1=C(S(=O)(=O)NCC2=NC(=O)O[N-]2)SC=N1 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.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 14, 11, 11, 8, 5, 1, 8, 1, 11, 12, 8, 14, 1, 8, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 6, 6, 4, 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: [13, 13, 1, 13, 1, 1, 1, 12, 12, 12, 22, 61, 152, 152, 152, 152, 152, 1, 1, 1, 13, 13, 13, 22, 61, 61, 1] 201 rigid atoms, others: [2, 4, 5, 6, 17, 18, 19, 26] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25]) 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: REAL300025569588 none COC(=O)C1=C(S(=O)(=O)NCC2=NC(=O)O[N-]2)SC=N1 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.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 14, 11, 11, 8, 5, 1, 8, 1, 11, 12, 8, 14, 1, 8, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 6, 6, 4, 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, 152, 201, 152, 85, 47, 85, 85, 8, 1, 1, 1, 1, 1, 1, 1, 152, 152, 152, 201, 201, 201, 47, 8, 8, 152] 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: 626 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901151/working/building/REAL300025569588 /scratch/stefan/7901151/working /scratch/stefan/7901151 Finished preparing REAL300025569588 Recording results /scratch/stefan/7901151/working /scratch/stefan/7901151 Appending to /scratch/stefan/7901151/finished/xaaaaat_worked.* 0: /scratch/stefan/7901151/working/building/REAL300025569588/0.* 1: /scratch/stefan/7901151/working/building/REAL300025569588/1.* Removing working files in /scratch/stefan/7901151/working/building/REAL300025569588 Building REAL300025569589 mkdir: created directory `/scratch/stefan/7901151/working/building/REAL300025569589' /scratch/stefan/7901151/working/building/REAL300025569589 /scratch/stefan/7901151/working /scratch/stefan/7901151 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025569589 mkdir: created directory `0' /scratch/stefan/7901151/working/building/REAL300025569589/0 /scratch/stefan/7901151/working/building/REAL300025569589 /scratch/stefan/7901151/working /scratch/stefan/7901151 Protomer 0 (index: 92) Found valid previously generated 3D confromation in /scratch/stefan/7901151/working/3D/92 `/scratch/stefan/7901151/working/3D/92' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(F)=CC(S(=O)(=O)NCC2=NC(=O)O[N-]2)=C1) `REAL300025569589.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025569589.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901151/working/building/REAL300025569589/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569589 none COC(=O)C1=CC(F)=CC(S(=O)(=O)NCC2=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', 'F', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 15, 1, 1, 14, 11, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 6, 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, 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: [12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 29, 128, 128, 128, 128, 128, 1, 13, 13, 13, 1, 1, 9, 29, 29, 1] 201 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 21, 25, 26, 30] set([0, 1, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 27, 28, 29]) total number of confs: 266 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569589 none COC(=O)C1=CC(F)=CC(S(=O)(=O)NCC2=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', 'F', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 15, 1, 1, 14, 11, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 6, 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, 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, 128, 201, 128, 128, 128, 128, 128, 70, 42, 70, 70, 8, 1, 1, 1, 1, 1, 1, 1, 128, 201, 201, 201, 128, 128, 42, 8, 8, 128] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 677 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901151/working/building/REAL300025569589 /scratch/stefan/7901151/working /scratch/stefan/7901151 Finished preparing REAL300025569589 Recording results /scratch/stefan/7901151/working /scratch/stefan/7901151 Appending to /scratch/stefan/7901151/finished/xaaaaat_worked.* 0: /scratch/stefan/7901151/working/building/REAL300025569589/0.* Removing working files in /scratch/stefan/7901151/working/building/REAL300025569589 Building REAL300025569590 mkdir: created directory `/scratch/stefan/7901151/working/building/REAL300025569590' /scratch/stefan/7901151/working/building/REAL300025569590 /scratch/stefan/7901151/working /scratch/stefan/7901151 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025569590 mkdir: created directory `0' /scratch/stefan/7901151/working/building/REAL300025569590/0 /scratch/stefan/7901151/working/building/REAL300025569590 /scratch/stefan/7901151/working /scratch/stefan/7901151 Protomer 0 (index: 93) Found valid previously generated 3D confromation in /scratch/stefan/7901151/working/3D/93 `/scratch/stefan/7901151/working/3D/93' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CNS(=O)(=O)CC2=NOC3=CC=CC=C32)[N-]O1) `REAL300025569590.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025569590.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901151/working/building/REAL300025569590/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569590 none O=C1N=C(CNS(=O)(=O)CC2=NOC3=CC=CC=C32)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'N.2', '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'] dock atom type numbers: [11, 1, 8, 1, 5, 8, 14, 11, 11, 5, 1, 8, 12, 1, 1, 1, 1, 1, 1, 8, 12, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in 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, 54, 103, 103, 103, 167, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 9, 9, 54, 167, 167, 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: 801 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569590 none O=C1N=C(CNS(=O)(=O)CC2=NOC3=CC=CC=C32)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'N.2', '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'] dock atom type numbers: [11, 1, 8, 1, 5, 8, 14, 11, 11, 5, 1, 8, 12, 1, 1, 1, 1, 1, 1, 8, 12, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 45, 17, 5, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 125, 125, 45, 5, 5, 1, 1, 1, 1] 201 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 635 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901151/working/building/REAL300025569590 /scratch/stefan/7901151/working /scratch/stefan/7901151 Finished preparing REAL300025569590 Recording results /scratch/stefan/7901151/working /scratch/stefan/7901151 Appending to /scratch/stefan/7901151/finished/xaaaaat_worked.* 0: /scratch/stefan/7901151/working/building/REAL300025569590/0.* Removing working files in /scratch/stefan/7901151/working/building/REAL300025569590 Building REAL300025569591 mkdir: created directory `/scratch/stefan/7901151/working/building/REAL300025569591' /scratch/stefan/7901151/working/building/REAL300025569591 /scratch/stefan/7901151/working /scratch/stefan/7901151 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025569591 mkdir: created directory `0' /scratch/stefan/7901151/working/building/REAL300025569591/0 /scratch/stefan/7901151/working/building/REAL300025569591 /scratch/stefan/7901151/working /scratch/stefan/7901151 Protomer 0 (index: 94) Found valid previously generated 3D confromation in /scratch/stefan/7901151/working/3D/94 `/scratch/stefan/7901151/working/3D/94' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1CC2=CC(S(=O)(=O)NCC3=NC(=O)O[N-]3)=CC3=C2N1CCC3) `REAL300025569591.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025569591.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901151/working/building/REAL300025569591/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569591 none O=C1CC2=CC(S(=O)(=O)NCC3=NC(=O)O[N-]3)=CC3=C2N1CCC3 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 14, 11, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 8, 5, 5, 5, 7, 7, 7, 6, 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, 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 108 conformations in input total number of sets (complete confs): 108 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 48, 108, 108, 108, 108, 108, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 48, 48, 1, 1, 1, 1, 1, 1, 1] 108 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 27, 28, 29]) 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: REAL300025569591 none O=C1CC2=CC(S(=O)(=O)NCC3=NC(=O)O[N-]3)=CC3=C2N1CCC3 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 14, 11, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 8, 5, 5, 5, 7, 7, 7, 6, 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, 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 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, 108, 108, 59, 37, 59, 59, 8, 1, 1, 1, 1, 1, 1, 1, 108, 108, 108, 108, 108, 108, 108, 108, 108, 108, 37, 8, 8, 108, 108, 108, 108, 108, 108, 108] 108 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 318 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901151/working/building/REAL300025569591 /scratch/stefan/7901151/working /scratch/stefan/7901151 Finished preparing REAL300025569591 Recording results /scratch/stefan/7901151/working /scratch/stefan/7901151 Appending to /scratch/stefan/7901151/finished/xaaaaat_worked.* 0: /scratch/stefan/7901151/working/building/REAL300025569591/0.* Removing working files in /scratch/stefan/7901151/working/building/REAL300025569591 Building REAL300025569592 mkdir: created directory `/scratch/stefan/7901151/working/building/REAL300025569592' /scratch/stefan/7901151/working/building/REAL300025569592 /scratch/stefan/7901151/working /scratch/stefan/7901151 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025569592 mkdir: created directory `0' /scratch/stefan/7901151/working/building/REAL300025569592/0 /scratch/stefan/7901151/working/building/REAL300025569592 /scratch/stefan/7901151/working /scratch/stefan/7901151 Protomer 0 (index: 95) Found valid previously generated 3D confromation in /scratch/stefan/7901151/working/3D/95 `/scratch/stefan/7901151/working/3D/95' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCN1N=C(C)C(S(=O)(=O)NCC2=NC(=O)O[N-]2)=C1C) `REAL300025569592.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025569592.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901151/working/building/REAL300025569592/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569592 none COCN1N=C(C)C(S(=O)(=O)NCC2=NC(=O)O[N-]2)=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [5, 12, 5, 8, 8, 1, 5, 1, 14, 11, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 5, 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, 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: [24, 7, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 14, 34, 117, 117, 117, 117, 117, 1, 1, 24, 24, 24, 7, 7, 2, 2, 2, 14, 34, 34, 2, 2, 2] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 19, 20] set([0, 1, 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: 299 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569592 none COCN1N=C(C)C(S(=O)(=O)NCC2=NC(=O)O[N-]2)=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [5, 12, 5, 8, 8, 1, 5, 1, 14, 11, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 5, 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, 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, 117, 117, 117, 117, 117, 66, 41, 66, 66, 8, 1, 1, 1, 1, 1, 1, 1, 117, 117, 201, 201, 201, 201, 201, 117, 117, 117, 41, 8, 8, 117, 117, 117] 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: 760 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901151/working/building/REAL300025569592 /scratch/stefan/7901151/working /scratch/stefan/7901151 Finished preparing REAL300025569592 Recording results /scratch/stefan/7901151/working /scratch/stefan/7901151 Appending to /scratch/stefan/7901151/finished/xaaaaat_worked.* 0: /scratch/stefan/7901151/working/building/REAL300025569592/0.* Removing working files in /scratch/stefan/7901151/working/building/REAL300025569592 Building REAL300025569593 mkdir: created directory `/scratch/stefan/7901151/working/building/REAL300025569593' /scratch/stefan/7901151/working/building/REAL300025569593 /scratch/stefan/7901151/working /scratch/stefan/7901151 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025569593 mkdir: created directory `0' /scratch/stefan/7901151/working/building/REAL300025569593/0 /scratch/stefan/7901151/working/building/REAL300025569593 /scratch/stefan/7901151/working /scratch/stefan/7901151 Protomer 0 (index: 96) Found valid previously generated 3D confromation in /scratch/stefan/7901151/working/3D/96 `/scratch/stefan/7901151/working/3D/96' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(C1CCCC1)N1CC(S(=O)(=O)NCC2=NC(=O)O[N-]2)C1) `REAL300025569593.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025569593.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901151/working/building/REAL300025569593/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569593 none O=C(C1CCCC1)N1CC(S(=O)(=O)NCC2=NC(=O)O[N-]2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 5, 5, 5, 5, 5, 8, 5, 5, 14, 11, 11, 8, 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] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 1, 1, 1, 1, 1, 7, 12, 12, 12, 42, 42, 42, 90, 127, 201, 201, 201, 201, 201, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 90, 127, 127, 12, 12] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31, 32, 33, 34, 35, 36, 37, 38]) 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569593 none O=C(C1CCCC1)N1CC(S(=O)(=O)NCC2=NC(=O)O[N-]2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 5, 5, 5, 5, 5, 8, 5, 5, 14, 11, 11, 8, 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] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 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: [116, 110, 116, 201, 201, 201, 201, 110, 110, 66, 42, 66, 66, 8, 1, 1, 1, 1, 1, 1, 1, 110, 201, 201, 201, 201, 201, 201, 201, 201, 201, 110, 110, 110, 42, 8, 8, 110, 110] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 737 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569593 none O=C(C1CCCC1)N1CC(S(=O)(=O)NCC2=NC(=O)O[N-]2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 5, 5, 5, 5, 5, 8, 5, 5, 14, 11, 11, 8, 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] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 12, 12, 12, 12, 1, 1, 1, 1, 7, 7, 7, 21, 42, 110, 110, 110, 110, 110, 1, 12, 12, 12, 12, 12, 12, 12, 12, 12, 1, 1, 1, 21, 42, 42, 1, 1] 201 rigid atoms, others: [32, 1, 33, 38, 7, 8, 9, 10, 21, 37, 31] set([0, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36]) total number of confs: 295 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901151/working/building/REAL300025569593 /scratch/stefan/7901151/working /scratch/stefan/7901151 Finished preparing REAL300025569593 Recording results /scratch/stefan/7901151/working /scratch/stefan/7901151 Appending to /scratch/stefan/7901151/finished/xaaaaat_worked.* 0: /scratch/stefan/7901151/working/building/REAL300025569593/0.* Removing working files in /scratch/stefan/7901151/working/building/REAL300025569593 Building REAL300025569594 mkdir: created directory `/scratch/stefan/7901151/working/building/REAL300025569594' /scratch/stefan/7901151/working/building/REAL300025569594 /scratch/stefan/7901151/working /scratch/stefan/7901151 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025569594 mkdir: created directory `0' /scratch/stefan/7901151/working/building/REAL300025569594/0 /scratch/stefan/7901151/working/building/REAL300025569594 /scratch/stefan/7901151/working /scratch/stefan/7901151 Protomer 0 (index: 97) Found valid previously generated 3D confromation in /scratch/stefan/7901151/working/3D/97 `/scratch/stefan/7901151/working/3D/97' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(CC(C)C)C(C)=C1S(=O)(=O)NCC1=NC(=O)O[N-]1) `REAL300025569594.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025569594.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901151/working/building/REAL300025569594/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569594 none CC1=NN(CC(C)C)C(C)=C1S(=O)(=O)NCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.2', 'N.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, 5, 1, 5, 1, 14, 11, 11, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 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, 5, 1, 1, 1, 1, 10, 10, 10, 18, 48, 133, 133, 133, 133, 133, 2, 2, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 2, 2, 18, 48, 48] 201 rigid atoms, others: [0, 1, 2, 3, 4, 8, 9, 10, 11] set([5, 6, 7, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 336 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569594 none CC1=NN(CC(C)C)C(C)=C1S(=O)(=O)NCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.2', 'N.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, 5, 1, 5, 1, 14, 11, 11, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 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: [133, 133, 133, 133, 133, 201, 201, 201, 133, 133, 97, 48, 97, 97, 8, 1, 1, 1, 1, 1, 1, 1, 133, 133, 133, 201, 201, 201, 201, 201, 201, 201, 201, 201, 133, 133, 133, 48, 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: 834 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901151/working/building/REAL300025569594 /scratch/stefan/7901151/working /scratch/stefan/7901151 Finished preparing REAL300025569594 Recording results /scratch/stefan/7901151/working /scratch/stefan/7901151 Appending to /scratch/stefan/7901151/finished/xaaaaat_worked.* 0: /scratch/stefan/7901151/working/building/REAL300025569594/0.* Removing working files in /scratch/stefan/7901151/working/building/REAL300025569594 Building REAL300025569595 mkdir: created directory `/scratch/stefan/7901151/working/building/REAL300025569595' /scratch/stefan/7901151/working/building/REAL300025569595 /scratch/stefan/7901151/working /scratch/stefan/7901151 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025569595 mkdir: created directory `0' /scratch/stefan/7901151/working/building/REAL300025569595/0 /scratch/stefan/7901151/working/building/REAL300025569595 /scratch/stefan/7901151/working /scratch/stefan/7901151 Protomer 0 (index: 98) Found valid previously generated 3D confromation in /scratch/stefan/7901151/working/3D/98 `/scratch/stefan/7901151/working/3D/98' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(C1=CC=CC=C1)N1CCCC(S(=O)(=O)NCC2=NC(=O)O[N-]2)C1) `REAL300025569595.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025569595.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901151/working/building/REAL300025569595/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569595 none O=C(C1=CC=CC=C1)N1CCCC(S(=O)(=O)NCC2=NC(=O)O[N-]2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 14, 11, 11, 8, 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] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 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, 6, 13, 13, 13, 13, 13, 40, 40, 40, 79, 127, 201, 201, 201, 201, 201, 13, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13, 79, 127, 127, 13, 13] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 25, 26, 27, 28, 29] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 622 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569595 none O=C(C1=CC=CC=C1)N1CCCC(S(=O)(=O)NCC2=NC(=O)O[N-]2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 14, 11, 11, 8, 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] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 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, 135, 201, 201, 201, 201, 201, 201, 135, 135, 135, 135, 98, 49, 98, 98, 8, 1, 1, 1, 1, 1, 1, 1, 135, 201, 201, 201, 201, 201, 135, 135, 135, 135, 135, 135, 135, 49, 8, 8, 135, 135] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 702 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569595 none O=C(C1=CC=CC=C1)N1CCCC(S(=O)(=O)NCC2=NC(=O)O[N-]2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 14, 11, 11, 8, 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] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 13, 13, 7, 13, 13, 1, 1, 1, 1, 1, 1, 8, 8, 8, 23, 55, 135, 135, 135, 135, 135, 1, 13, 13, 8, 13, 13, 1, 1, 1, 1, 1, 1, 1, 23, 55, 55, 1, 1] 201 rigid atoms, others: [32, 1, 34, 35, 36, 33, 8, 9, 10, 11, 12, 13, 40, 41, 24, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 37, 38, 39]) total number of confs: 366 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901151/working/building/REAL300025569595 /scratch/stefan/7901151/working /scratch/stefan/7901151 Finished preparing REAL300025569595 Recording results /scratch/stefan/7901151/working /scratch/stefan/7901151 Appending to /scratch/stefan/7901151/finished/xaaaaat_worked.* 0: /scratch/stefan/7901151/working/building/REAL300025569595/0.* Removing working files in /scratch/stefan/7901151/working/building/REAL300025569595 Building REAL300025569596 mkdir: created directory `/scratch/stefan/7901151/working/building/REAL300025569596' /scratch/stefan/7901151/working/building/REAL300025569596 /scratch/stefan/7901151/working /scratch/stefan/7901151 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025569596 mkdir: created directory `0' /scratch/stefan/7901151/working/building/REAL300025569596/0 /scratch/stefan/7901151/working/building/REAL300025569596 /scratch/stefan/7901151/working /scratch/stefan/7901151 Protomer 0 (index: 99) Found valid previously generated 3D confromation in /scratch/stefan/7901151/working/3D/99 `/scratch/stefan/7901151/working/3D/99' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C1N=C(CNS(=O)(=O)C2=CC=C(OCC(F)F)C=C2)[N-]O1) `REAL300025569596.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025569596.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901151/working/building/REAL300025569596/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569596 none O=C1N=C(CNS(=O)(=O)C2=CC=C(OCC(F)F)C=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', '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', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 5, 15, 15, 1, 1, 8, 12, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 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, 43, 65, 65, 65, 65, 65, 65, 65, 185, 193, 201, 201, 65, 65, 1, 1, 9, 9, 43, 65, 65, 193, 193, 201, 65, 65] 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: 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: REAL300025569596 none O=C1N=C(CNS(=O)(=O)C2=CC=C(OCC(F)F)C=C2)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.2', 'C.2', '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', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 5, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 5, 15, 15, 1, 1, 8, 12, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 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: [65, 65, 65, 17, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 8, 27, 27, 1, 1, 65, 65, 17, 17, 5, 1, 1, 9, 9, 27, 1, 1] 201 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 18, 19, 25, 26, 30, 31] set([0, 1, 2, 3, 4, 14, 15, 16, 17, 20, 21, 22, 23, 24, 27, 28, 29]) total number of confs: 226 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901151/working/building/REAL300025569596 /scratch/stefan/7901151/working /scratch/stefan/7901151 Finished preparing REAL300025569596 Recording results /scratch/stefan/7901151/working /scratch/stefan/7901151 Appending to /scratch/stefan/7901151/finished/xaaaaat_worked.* 0: /scratch/stefan/7901151/working/building/REAL300025569596/0.* Removing working files in /scratch/stefan/7901151/working/building/REAL300025569596 Building REAL300025569597 mkdir: created directory `/scratch/stefan/7901151/working/building/REAL300025569597' /scratch/stefan/7901151/working/building/REAL300025569597 /scratch/stefan/7901151/working /scratch/stefan/7901151 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025569597 mkdir: created directory `0' /scratch/stefan/7901151/working/building/REAL300025569597/0 /scratch/stefan/7901151/working/building/REAL300025569597 /scratch/stefan/7901151/working /scratch/stefan/7901151 Protomer 0 (index: 100) Found valid previously generated 3D confromation in /scratch/stefan/7901151/working/3D/100 `/scratch/stefan/7901151/working/3D/100' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1CCCCC1S(=O)(=O)NCC1=NC(=O)O[N-]1) `REAL300025569597.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025569597.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901151/working/building/REAL300025569597/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569597 none COC(=O)C1CCCCC1S(=O)(=O)NCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.2', 'N.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, 12, 1, 11, 5, 5, 5, 5, 5, 5, 14, 11, 11, 8, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 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 157 conformations in input total number of sets (complete confs): 157 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 20, 57, 122, 122, 122, 122, 122, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 57, 57] 157 rigid atoms, others: [32, 33, 2, 4, 5, 6, 7, 8, 9, 10, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 34, 3, 36, 35, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23]) total number of confs: 325 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: REAL300025569597 none COC(=O)C1CCCCC1S(=O)(=O)NCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.2', 'N.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, 12, 1, 11, 5, 5, 5, 5, 5, 5, 14, 11, 11, 8, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 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 157 conformations in input total number of sets (complete confs): 157 using faster count positions algorithm for large data unique positions, atoms: [157, 157, 122, 157, 122, 122, 122, 122, 122, 88, 54, 88, 88, 8, 1, 1, 1, 1, 1, 1, 1, 157, 157, 157, 122, 122, 122, 122, 122, 122, 122, 122, 122, 122, 54, 8, 8] 157 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: 569 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901151/working/building/REAL300025569597 /scratch/stefan/7901151/working /scratch/stefan/7901151 Finished preparing REAL300025569597 Recording results /scratch/stefan/7901151/working /scratch/stefan/7901151 Appending to /scratch/stefan/7901151/finished/xaaaaat_worked.* 0: /scratch/stefan/7901151/working/building/REAL300025569597/0.* Removing working files in /scratch/stefan/7901151/working/building/REAL300025569597 Building REAL300025569598 mkdir: created directory `/scratch/stefan/7901151/working/building/REAL300025569598' /scratch/stefan/7901151/working/building/REAL300025569598 /scratch/stefan/7901151/working /scratch/stefan/7901151 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025569598 mkdir: created directory `0' /scratch/stefan/7901151/working/building/REAL300025569598/0 /scratch/stefan/7901151/working/building/REAL300025569598 /scratch/stefan/7901151/working /scratch/stefan/7901151 Protomer 0 (index: 101) Found valid previously generated 3D confromation in /scratch/stefan/7901151/working/3D/101 `/scratch/stefan/7901151/working/3D/101' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C(S(=O)(=O)NCC2=NC(=O)O[N-]2)C(Cl)=C1) `REAL300025569598.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025569598.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901151/working/building/REAL300025569598/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569598 none N#CC1=CC=C(S(=O)(=O)NCC2=NC(=O)O[N-]2)C(Cl)=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.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 16, 1, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 5, 3, 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, 5, 5, 5, 9, 25, 63, 63, 63, 63, 63, 1, 1, 1, 1, 1, 9, 25, 25, 1] 63 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 17, 18, 19, 20, 21, 25] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569598 none N#CC1=CC=C(S(=O)(=O)NCC2=NC(=O)O[N-]2)C(Cl)=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.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 16, 1, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 5, 3, 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, 61, 45, 61, 61, 8, 1, 1, 1, 1, 1, 1, 1, 63, 63, 63, 63, 63, 45, 8, 8, 63] 63 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]) total number of confs: 215 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901151/working/building/REAL300025569598 /scratch/stefan/7901151/working /scratch/stefan/7901151 Finished preparing REAL300025569598 Recording results /scratch/stefan/7901151/working /scratch/stefan/7901151 Appending to /scratch/stefan/7901151/finished/xaaaaat_worked.* 0: /scratch/stefan/7901151/working/building/REAL300025569598/0.* Removing working files in /scratch/stefan/7901151/working/building/REAL300025569598 Building REAL300025569599 mkdir: created directory `/scratch/stefan/7901151/working/building/REAL300025569599' /scratch/stefan/7901151/working/building/REAL300025569599 /scratch/stefan/7901151/working /scratch/stefan/7901151 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025569599 mkdir: created directory `0' /scratch/stefan/7901151/working/building/REAL300025569599/0 /scratch/stefan/7901151/working/building/REAL300025569599 /scratch/stefan/7901151/working /scratch/stefan/7901151 Protomer 0 (index: 102) Found valid previously generated 3D confromation in /scratch/stefan/7901151/working/3D/102 `/scratch/stefan/7901151/working/3D/102' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(Br)=C(F)C=C1S(=O)(=O)NCC1=NC(=O)O[N-]1) `REAL300025569599.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025569599.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901151/working/building/REAL300025569599/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569599 none COC1=CC(Br)=C(F)C=C1S(=O)(=O)NCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 17, 1, 15, 1, 1, 14, 11, 11, 8, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 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: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 25, 74, 199, 199, 199, 199, 199, 4, 4, 4, 1, 1, 25, 74, 74] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 24, 25] set([0, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28]) 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: REAL300025569599 none COC1=CC(Br)=C(F)C=C1S(=O)(=O)NCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 17, 1, 15, 1, 1, 14, 11, 11, 8, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 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, 199, 199, 199, 170, 171, 199, 199, 199, 128, 53, 128, 128, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 199, 199, 53, 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: 700 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901151/working/building/REAL300025569599 /scratch/stefan/7901151/working /scratch/stefan/7901151 Finished preparing REAL300025569599 Recording results /scratch/stefan/7901151/working /scratch/stefan/7901151 Appending to /scratch/stefan/7901151/finished/xaaaaat_worked.* 0: /scratch/stefan/7901151/working/building/REAL300025569599/0.* Removing working files in /scratch/stefan/7901151/working/building/REAL300025569599 Building REAL300025569600 mkdir: created directory `/scratch/stefan/7901151/working/building/REAL300025569600' /scratch/stefan/7901151/working/building/REAL300025569600 /scratch/stefan/7901151/working /scratch/stefan/7901151 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025569600 mkdir: created directory `0' /scratch/stefan/7901151/working/building/REAL300025569600/0 /scratch/stefan/7901151/working/building/REAL300025569600 /scratch/stefan/7901151/working /scratch/stefan/7901151 Protomer 0 (index: 103) Found valid previously generated 3D confromation in /scratch/stefan/7901151/working/3D/103 `/scratch/stefan/7901151/working/3D/103' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(C1=CC=CC(Cl)=C1)N1CC(S(=O)(=O)NCC2=NC(=O)O[N-]2)C1) `REAL300025569600.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025569600.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901151/working/building/REAL300025569600/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569600 none O=C(C1=CC=CC(Cl)=C1)N1CC(S(=O)(=O)NCC2=NC(=O)O[N-]2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.am', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [11, 1, 1, 1, 1, 1, 1, 16, 1, 8, 5, 5, 14, 11, 11, 8, 5, 1, 8, 1, 11, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 1, 1, 1, 1, 1, 1, 1, 11, 17, 17, 17, 39, 39, 39, 76, 111, 201, 201, 201, 201, 201, 17, 1, 1, 1, 1, 17, 17, 17, 76, 111, 111, 17, 17] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 24, 25, 26, 27] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35]) 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569600 none O=C(C1=CC=CC(Cl)=C1)N1CC(S(=O)(=O)NCC2=NC(=O)O[N-]2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.am', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [11, 1, 1, 1, 1, 1, 1, 16, 1, 8, 5, 5, 14, 11, 11, 8, 5, 1, 8, 1, 11, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 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: [109, 101, 109, 201, 201, 201, 201, 201, 201, 101, 101, 57, 39, 57, 57, 8, 1, 1, 1, 1, 1, 1, 1, 101, 201, 201, 201, 201, 101, 101, 101, 39, 8, 8, 101, 101] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 532 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025569600 none O=C(C1=CC=CC(Cl)=C1)N1CC(S(=O)(=O)NCC2=NC(=O)O[N-]2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.am', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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'] dock atom type numbers: [11, 1, 1, 1, 1, 1, 1, 16, 1, 8, 5, 5, 14, 11, 11, 8, 5, 1, 8, 1, 11, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 7, 7, 7, 19, 35, 101, 101, 101, 101, 101, 1, 17, 17, 17, 17, 1, 1, 1, 19, 35, 35, 1, 1] 201 rigid atoms, others: [1, 34, 35, 9, 10, 11, 12, 23, 28, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 31, 32, 33]) total number of confs: 257 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901151/working/building/REAL300025569600 /scratch/stefan/7901151/working /scratch/stefan/7901151 Finished preparing REAL300025569600 Recording results /scratch/stefan/7901151/working /scratch/stefan/7901151 Appending to /scratch/stefan/7901151/finished/xaaaaat_worked.* 0: /scratch/stefan/7901151/working/building/REAL300025569600/0.* Removing working files in /scratch/stefan/7901151/working/building/REAL300025569600 /scratch/stefan/7901151 Compressing combined databse files /scratch/stefan/7901151/finished/xaaaaat_worked.db2.gz /scratch/stefan/7901151/finished/xaaaaat_worked.solv.gz ======================================================= WARNING: STORE_PROTOMERS not executable or a directory! All results left in place (/scratch/stefan/7901151/finished) ======================================================= Finalizing... removed `/scratch/stefan/7901151/working/3D/104' removed directory: `/scratch/stefan/7901151/working/3D' rmdir: removing directory, `/scratch/stefan/7901151/working/building' rmdir: removing directory, `/scratch/stefan/7901151/working' ls: No match. ls: No match.